From bf071cd4460fbbc597d5096ab7976b53ffc88d5e Mon Sep 17 00:00:00 2001 From: erinkoreilly Date: Fri, 8 Mar 2024 11:07:28 -0800 Subject: [PATCH] rerender --- docs/emlab-workflow-and-platforms.html | 10 +++++----- docs/search_index.json | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/emlab-workflow-and-platforms.html b/docs/emlab-workflow-and-platforms.html index 2df4263..1b2ad0b 100644 --- a/docs/emlab-workflow-and-platforms.html +++ b/docs/emlab-workflow-and-platforms.html @@ -402,7 +402,7 @@

8.6 Nextcloud and the emLab serve

8.6.1 Signing up for an account with GRIT

If you do not yet have a GRIT account

    -
  1. Fill out the GRIT compute access request form (CARF): +
  2. Fill out the GRIT compute access request form (CARF): https://forms.gle/kqzttgMAjzt867FZA
    • Under “Faculty” put: Christopher Costello
    • Under “Research Group Name” put: emLab
      • @@ -410,14 +410,14 @@

      8.6.1 Signing up for an account w
    • Note: If you are a member of the Waitt team in addition to the above add: emLab Waitt group membership

  3. You should receive an email from GRIT saying that your account has been created. Follow any additional instructions provided by GRIT.

    4. -

  4. Create your GRIT access credentials at the following link: . The username and password you use here will be the same username and password for accessing the Nextcloud data directories and emLab servers.

    5. +

  5. Create your GRIT access credentials at the following link: https://dc1.grit.ucsb.edu/. The username and password you use here will be the same username and password for accessing the Nextcloud data directories and emLab servers.

If you already have a GRIT account but are not connected to the emLab group

  1. Send a help ticket email to GRIT (). Say that you are part of the emLab research group, which has Christopher Costello as the faculty PI. Ask them to please connect the email to the emLab group membership (for accessing emLab data storage space and emLab computational servers, including quebracho and sequoia) and Nextcloud group membership. Follow any additional instructions provided by GRIT.

    2. -

  2. Create your GRIT access credentials at the following link: . The username and password you use here will be the same username and password for accessing the Nextcloud data directories and emLab servers.

    3. +

  3. Create your GRIT access credentials at the following link: https://dc1.grit.ucsb.edu/. The username and password you use here will be the same username and password for accessing the Nextcloud data directories and emLab servers.

-

If you ever need to reset your password, you can use the following link: .

+

If you ever need to reset your password, you can use the following link: https://selfservice.grit.ucsb.edu/.

8.6.2 Setting up Nextcloud on your local machine

@@ -462,7 +462,7 @@

8.6.2.2 Configuring how the Nextc
  • Cons
    • Synced directories will take up space on your local machine. Since many of our directories are quite large, you will need to ensure you have sufficient hard drive space to sync the directories you want.
      • -
    • You will not be able to view the full emLab directory structure on your local machine. However, you can always view the entire directory structure using the Nextcloud browser interface:
      • +
    • You will not be able to view the full emLab directory structure on your local machine. However, you can always view the entire directory structure using the Nextcloud browser interface: https://nextcloud.grit.ucsb.edu/index.php/apps/files
    • Whenever you join projects or leave projects, you will need to manually selectively sync directories onto your local machine as needed. So this will require some level of continual effort to ensure the right directories and files are synced.
    • diff --git a/docs/search_index.json b/docs/search_index.json index b5b1c87..a3a99ca 100644 --- a/docs/search_index.json +++ b/docs/search_index.json @@ -6,7 +6,7 @@ ["expectations.html", "Section 5 Expectations 5.1 Work environment 5.2 Time management 5.3 Project roles 5.4 Meetings and events", " Section 5 Expectations 5.1 Work environment Principles for creating a hybrid schedule for emLab We are excited for emLab to adopt a hybrid schedule starting this fall so that the emLab community can use campus and our offices as a tool for supporting connection, community and culture across our team. In thinking about what kind of working model and balance between remote and in-person work would best support the emLab community, we considered our mission, values and culture, learned from the hybrid pilots over the past year and used data and information about hybrid and remote work (e.g., Adam Grant’s podcast). One of emLab’s main goals is to build a vibrant intellectual community of people to collaborate on innovative, impactful research. As a team who iterates together on ideas, research, writing and coding, spending time together in the office is important to support this flow of ideas and information. We each balance both team oriented activities and tasks with individual tasks, so having time to focus on individual work is also important. We provide guidance below on the structure of the hybrid schedule, and realize that remaining flexible and adapting as needed is essential as we all try to navigate this phase of pandemic life together in the best way possible. Overview of the hybrid model emLab will return to in-person work starting the week of September 12. All Santa Barbara-based team members will be expected to work from campus Tuesday - Wednesday and have the option to work remotely Monday, Thursday, and Friday. Take advantage of in person/on campus days for things like: internal team meetings, structured and unstructured time with your project teams, brainstorming sessions, walking and running meetings, collaborative writing, working sessions, troubleshooting with colleagues, white board sessions, etc. Take advantage of remote days for things like: focused work, ‘deep’ work, coding, focused writing, 1:1 meetings that don’t fit in other days, etc All Santa Barbara-based team members will have assigned office space on the UCSB campus. Logistics Meetings All-team meetings and events will take place on in-person team days emLab’s “MMM” will move to Tuesdays from 9:30 -10 am - now called emLab Tuesday Team Time (TTT) emLab watercoolers will be held on Wednesdays or Thursdays emLab/Environmental Resource Economics (ERE) seminars will be held on Thursdays emLab lunches are returning in a new form - this will be a casual, informal time to have lunch and catch up with colleagues on Decker’s Deck. Note: emLab lunches will be Wednesdays from 12-1 pm. emLab will provide lunch for everyone for the first month we are in-person and after that, it will transition to a brown bag lunch. Zoom/remote meetings on in-person days We work with lots of collaborators and partners around the world, so it is likely you may also have zoom calls on in-person days. Here are some options and suggestions for hybrid/zoom meetings: MSI 1304 is available to reserve for zoom meetings - add bren-sfg@ucsb.edu to any calendar invite to reserve the room Bren Hall has 7 conference rooms of varying sizes that you can book up to 14 days in advance. For full details on MSI and Bren conference room sign-ups, see the emLab manual Call in via phone and take it outside/walking If someone on the call has a solo office, plan to take the call from their office Calls can also be taken from shared offices - everyone should have access to noise canceling headphones, so just give your office mates a heads up if you’re going to be jumping on a call/zoom. Hours and remote work All team members are responsible for setting their own hours within the work week and getting their work done on time in coordination with their project teams. Please use your google calendar to communicate to the team when you are not available during the work week. Individuals are welcome to work, send emails, etc. outside of ‘normal’ working hours (e.g., nights and weekends) but immediate responses are not expected outside of normal working hours Ad hoc remote work may be permitted on a case-by-case basis. Contact your supervisor to discuss and get approval for ad hoc remote working days and communicate/coordinate with your project teams as needed. Equipment and commuting emLab will provide equipment for one workstation that will include: a laptop or desktop computer, a bluetooth keyboard and mouse, up to two computer monitors, and noise canceling headphones. emLab will also provide a desk and chair in your university office, and miscellaneous office supplies (notebooks, pens, etc.) as needed. Please notify your supervisor for approval and contact Erin to assist with re-allocation or purchasing if you need any of the items listed above. The University provides these resources (TAP) for commuting to and from campus. Fully remote team members emLab team members will be based at the UCSB campus unless you have a previously agreed-upon arrangement with your supervisor. Exceptions to this may be granted on an as-needed basis for projects requiring remote work. COVID protocols for working from the office Please do not come into the office if you are exhibiting any symptoms at all, have recently been exposed to covid or are not feeling 100%. Information about where you can go for both asymptomatic and symptomatic testing is here. We will follow UCSB masking requirements and recommendations. The current policies and campus updates are posted here. Here is the current guidance: Effective June 13, masks are no longer required but are strongly recommended in indoor spaces on campus, regardless of vaccination status, except when working alone in private offices. All Santa Barbara-based employees must be fully vaccinated and have submitted proof of vaccination through the University here or have received an approved exemption before they will be allowed in any UC facility or office or to participate in any University programs. All employees must also complete the “COVID-19 Returning to Work” training course required by Cal/OSHA, which is available through the UC Learning Center. Please abide by University guidance related to COVID precautions for in-office work and in-person meetings. Cleaning materials and hand sanitizers will be available for office use. Guests and visitors Guests and visitors should follow the University’s COVID-19 interim visitor’s protocol. A few key points: Individuals invited to campus should be fully vaccinated against COVID-19 or have received a negative COVID-19 test result within 48 hours prior to their visit for a PCR test, or 24 hours prior for a rapid antigen home test. All visitors to campus are strongly recommended to wear face masks in any indoor space, and any individual who has symptoms suggestive of COVID-19 should avoid campus altogether. If you are unsure of a visitor’s vaccination status or prefer not to ask, you may send them the on-demand screening survey in advance to determine if they are cleared to be on campus and if and when they are required to test prior to arriving on campus, wear a mask or quarantine. The health and safety of our team remains the most important thing above all else. As we learned these past couple of years, things can rapidly change, and we will continue to adapt as needed. If you do not feel safe coming into the office or if you have suggestions on additional measures that you would like to see in place, please come talk to me, any member of the Leadership Team, or your supervisor. Exceptions to these guidelines are permitted after they have been discussed and approved by your supervisor. Please reach out to your supervisor or any member of the leadership team if you have any questions. Last updated: August 17, 2022 5.2 Time management It is important for every individual to understand and manage their workloads and responsibilities, and to ask for help when it is needed. Team members should prioritize the tasks that are most important and urgent. If you are having challenges prioritizing tasks, speak with your supervisor to discuss priorities. emLab project staff are allocated to one or more projects, which is likely to shift over time as projects come to completion and new projects are launched. Staff should be aware of their general percentage time allocation across projects, which are tracked in the project tracking sheet in Drive. Due to the adaptive nature of our work, these percentages are likely to vary daily, weekly or monthly, and should be used as guidelines rather than strict allocations. If staff are feeling either underutilized or overstretched, they should speak with their supervisor. 5.3 Project roles Principal Investigators Coming soon Research Staff Coming soon Project Managers Coming soon Postdoctoral Researchers Coming soon Graduate Students Coming soon Undergraduate Students Coming soon 5.4 Meetings and events emLab hosts a variety of events to foster a deep sense of community across roles and programs, and provide opportunities for our team to be as collaborative, functional, and fully integrated as possible. Each meeting or event aims to support the emLab mission of developing innovative insights and performing collaborative research, and supports one of the following objectives: facilitating research, building community, and informing & updating. We know things can come up that sometimes make it impossible to join everything, but we want to clarify that we do expect everyone to do their best to participate in team events, particularly the Tuesday Team Time meetings. Beyond that, if you find yourself with a lot on your plate, please use your discretion to decide when your participation will yield high returns, and do not feel obligated to participate in events that you don’t think will be a valuable use of your time. Each of us has unique interests, areas of expertise, and professional goals, and we trust that those will inform the decisions you make for yourself! Events organizers include: emLab operations team Executive Director - Michaela Clemence Program Manager - Erin O’Reilly Projects & Student Engagement Manager - Jennifer Bone Events & Project Manager - Heather Lahr Partnerships & Grants Manager - Annie Lovell Rotating faculty representatives (2023): Andrew Plantinga Antony Millner Here’s an overview of emLab events and the objectives of each, items with a * are highly encouraged: Meetings Meetings that facilitate the day-to-day workings on emLab. These serve as information conduits from leadership to staff as well as staff-to-staff support and collaboration. These are organized by the emLab operations team. *Tuesday Team Time (TTT) Who: emLab staff and postdocs Cadence: weekly on Tuesdays Structure: Learn about current work at emLab, celebrate successes, share team-wide announcements. 15 minute presentation by an emLab team member, 5 minutes of operational updates and announcements, and 10 minutes of team shoutouts, roundtable updates (on the first Monday of the month), or mingling. Detailed guidelines live here and the schedule lives here POC: Events Manager Project Management Meetings Who: Executive Director and project managers Cadence: monthly on the second Tuesday of the month Structure: Project managers fill our monthly status report prior to the meeting. Provide updates on the status of current projects, discuss challenges, and brainstorm solutions. POC: Executive Director Quarterly fundraising update Who: Executive Director and project and operations staff Cadence: quarterly Structure: Review funding pipeline and upcoming projects. POC: Partnerships & Grants Manager Community events Events geared towards community building and dissemination of information. *Team lunches Who: PIs, staff, postdocs, vistors Cadence: monthly on the first Tuesday of the month Aim: Monthly appreciation and collaboration catered lunches. This is a great time to share ideas and engage across the team. POC: Partnerships & Grants Manager Happy hours Who: PIs, staff, postdocs, visitors, students Cadence: variable Aim: Welcome new faces, celebrate successes, say goodbye to people transitioning away from emLab. POC: Events Manager emLab retreat Who: PIs, staff, postdocs Cadence: every 2 years Aim: Foster collaboration, align priorities, look ahead to emLab goals, celebrate successes. POC: Executive Director/Program Manager Holiday celebration Who: PIs, staff, postdocs, visitors, students Cadence: annually in December Typically hosted at a PI residence and may include gift exchange, games, and catered or potluck style food POC: Executive Director/Program Manager Academic events Events geared towards advancing current research, fostering collaboration, and networking to build stronger academics. These are organized by the Rotating Faculty Representatives and Events Manager. Research roundtable Who: emLab PIs, affiliates, postdocs, faculty collaborators What: Weekly lunch meeting to present, discuss, debate, and refine ideas and research questions. Guidelines and schedule can be found here. POC: Events Manager Environmental Resource Economics (ERE) Seminars Who: ERE Faculty, PhD students (bren, econ), postdocs, visitors What: Joint seminar with the Economics department. Up to 8 invited speakers per academic year. Here is an overview and planning checklist. POC: Events Manager Occasional Workshop What: Annual 1.5 day workshop for invited ERE researchers. Requires submission of papers and selection of presenters for full presentations and egg-timer presentations. Free registration for up to 100 total participants. POC: Events Manager UC-EE seminars What: Irregular remote seminars for 120+ UC Environmental, Energy and Natural Resource Economics faculty, postdoctoral scholars and graduate students. Requires addition to google group. Guidelines can be found here. POC: Projects & Student Engagement Manager "], ["feedback-and-learning.html", "Section 6 Feedback and learning 6.1 Overview of our feedback mentality 6.2 Career growth and professional development", " Section 6 Feedback and learning 6.1 Overview of our feedback mentality Fostering an environment that provides targeted and constructive feedback is an important part of promoting learning and growth, one of emLab’s core values. We endeavor to build a radically candid culture of feedback where we can challenge directly while also caring personally for one another. As we state in our code of conduct, good feedback is kind, respectful, clear, constructive, and focused on goals and values rather than personal preferences. We expect everyone on our team to give and receive feedback with gratitude and a growth mindset. We have created a number of internal emLab processes and structures to provide opportunities for individual and organizational feedback so that each of us, as well as emLab, can continue to learn and grow: Supervisor check-ins are held at a regular cadence (e.g., weekly, monthly) to provide mentorship, guidance, and feedback on day-to-day responsibilities and challenges as well as discuss longer term goals and professional development opportunities. Annual reviews are conducted each year with our project researchers, project managers, and operations team members to discuss and celebrate key accomplishments, provide targeted feedback, and discuss future goals. Team member exit interviews are conducted when team members leave to discuss their overall experience with emLab, and offer positive and constructive feedback for emLab. Monthly project management meetings are held with all emLab project managers to anticipate and workshop project changes and challenges and collectively and collaboratively improve emLab project management. Project exit interviews are held after the completion of every project to capture lessons learned, evaluate successes and challenges, and identify potential next steps. 6.2 Career growth and professional development 6.2.1 Recruiting top talent emLab aims to recruit and retain a diverse and cohesive team who thrive in an entrepreneurial setting, are adaptable, flexible problem solvers and embrace an open, generous, and collaborative approach. Our full recruiting process is outlined here. It includes information about who is involved in the recruiting process and how to decrease implicit bias at every stage of the process. Maintain a consistent onboarding process that is thoughtful and sets guidelines and expectations 6.2.2 Supervisor check-ins Supervisors provide mentorship, feedback, discuss professional development opportunities, etc. For any new staff, Executive Director proposes a supervisor and one or more Program Directors approves final decision Postdocs and researchers are supervised by emLab Principal Investigators or other researchers Project managers and operations staff are supervised by ED or other project management/operations staff The supervisor and employee should have regular check-ins at least monthly The purpose of these meetings is to first and foremost foster a relationship between the employee and supervisor. Potential items to discuss include: workload, task prioritization, problem solving advice, feedback on performance, professional development, and advancement opportunities. Supervisors and supervisees can utilize this individual mentoring plan template to guide conversations on feedback, goals and milestones. If using, individual mentoring plans should be revisited on quarterly basis. 6.2.3 Annual review process emLab holds annual reviews to provide a reciprocal forum for staff to receive feedback, answer any questions on their role, projects, and responsibilities, and discuss short- and long-term goals. This is a good opportunity for each employee to share their professional development goals and career aspirations with their supervisor, and identify ways that emLab can help each team member succeed with targeted support, training, or mentorship. The emLab annual review process is part of a broader strategy to foster a culture of growth and learning at emLab. emLab’s internal reviews include an emLab “Behaviorally Anchored Rating Scale (BARS)” assessment to help provide targeted and constructive feedback. The assessment focuses on four categories: 1) quality of work and time management, 2) creative problem-solving, adaptability, and innovation, 3) collaboration and teamwork, and 4) effective communication. These categories and the criteria they comprise are not necessarily comprehensive of all skills across the different roles on our team, but they represent core competencies that are critical to both individual and emLab productivity and performance. Process overview Annual reviews generally take place in the summer and are retrospective of the previous 12 months. Prior to their scheduled review, each team member will make a copy and fill out emLab’s annual review template in their own Drive and share a link with their supervisor. This template comprises a list of your accomplishments and the BARS assessment. A couple of notes on the assessment categories - these are designed for the purpose of learning and development, so everyone is likely to have areas of growth identified. We all have strengths and weaknesses, and the value of a process like this is offering constructive feedback so we can all continue to learn and grow. Conversely, assessments of ‘outstanding’ will likely be rare and given in cases of extraordinary contributions and performance. Your supervisor will also fill out the BARS assessment portion of the form simultaneously and will send it to you the day before your scheduled review. Your review will be led by your supervisor. In some cases, additional team members will join if you have worked closely with them over the past year. Annual review structure Reviews are generally about an hour long and are structured as follows: Accomplishments and outputs, strengths, and growth areas (~20 min). Walk through your accomplishments and BARS assessment, discussing (a) the following questions and (b) any instances where your self-assessment and supervisor assessment differed. What are the accomplishments you are most proud of over the past year? What aspects of your job do you most enjoy or feel you excel at? Where are your areas of growth and how can we work together to develop those? (Can include categories within or outside of the BARS categories) Work portfolio, expectations, and responsibilities (~20 min) Review your current project portfolio and discuss future projects (if applicable) Do you feel like you are being underutilized or overstretched across projects? Do you have any questions on what is expected of you in your role? Goals (~20 min). Discuss 1-3 goals in each of the following categories, steps or actions you can take towards these goals, and how we may be able to support you in achieving them. Short-term (6 months) Medium-term (1 - 2 years) Long-term (5 - 10 years) 6.2.4 University merit review process UCSB policies and procedures for all academic titles (e.g., faculty, Specialists, Academic Coordinators), including information about appointments and advancements are contained within academic personnel’s “Red Binder”. Please see this presentation for a distilled overview of UCSB’s merit review process for Specialist and Academic Coordinator series titles. Reach out to your supervisor in advance to discuss if you will be pursuing a merit increase and for resources as you draft your materials. 6.2.5 Speakers, classes, workshops, and mentorship opportunities There are lots of opportunities at Bren, MSI, and UCSB for continued growth and learning from visiting speakers to auditing courses to advising students and group projects. We are very supportive of these types of activities for personal and professional growth as long as you’re getting your work done. For opportunities with a bigger time commitment, like auditing a class or advising a Bren GP, please talk to your supervisor ahead of time to discuss a plan for balancing your project portfolio. 6.2.6 University and community resources EcoDataScience study group EcoDataScience is an environmental data science study group based at UCSB that offers opportunities for skill sharing, co-working, and community building. The group hosts sessions that teach coding and data analysis skills, often utilizing live-coding/interactive components. Previous sessions are available on GitHub (see the “Previous Sessions” section on the website for a full list). To join the group and receive updates regarding upcoming sessions, join the Google Group. The EcoDataScience Slack workspace is a great place to seek and share coding advice in real time. R-Ladies Santa Barbara R-Ladies Santa Barbara is a meet-up group for R-users of all proficiency levels who are interested in mentoring, networking, and expert upskilling. This community is designed to develop R skills and knowledge through social, collaborative learning, and sharing. To receive updates regarding upcoming events, join the group. UCSB Software Carpentry data science workshops The UCSB Library hosts a series of Software and Data Carpentry workshops that take place throughout the year. These guided and hands-on workshops focus on data science topics ranging from introductory Python courses to using R for spatial data analysis. Each workshop is designed for individuals with no previous knowledge on the topic. The workshops are also a great opportunity to engage with the broader UCSB data science community, as well as with the international Carpentries community that teaches foundational data science skills to researchers worldwide. These workshops are usually free for all UCSB undergraduate, staff, graduate students, and faculty researchers (in person workshops may charge a small fee to cover snacks). We encourage emLab staff to take advantage of these great workshops. In case you’re not able to join a workshop or are interested in past topics, all past UCSB workshop materials are available online. Content from additional workshops are available through the international Carpentries community for Data Carpentries, Software Carpentries, and [Library Carpentries](https://librarycarpentry.org/lessons/. The workshops that are hosted by the UCSB Library are chosen based on public demand. If there is a workshop that you are interested in that is not currently being taught, please reach out to library-collaboratory@ucsb.edu. Finally, if you are interested in getting involved and helping teach any of these courses, they are always looking for volunteers as helpers and instructors. To serve as a helper or instructor in a workshop, you will need to have experience in the workshop’s topic, but you do not need additional certifications. Feel free to reach out to Echelle Burns (mailto:echelle_burns@ucsb.edu) to learn more. "], ["project-selection-and-scoping.html", "Section 7 Project selection and scoping 7.1 Project selection criteria 7.2 Setting projects up for success in project scoping", " Section 7 Project selection and scoping 7.1 Project selection criteria emLab’s project development and selection criteria build on our mission and research identity to create guidelines for prioritizing the use of resources. The criteria are designed as a flexible tool, not a simple checklist or formula. To take on a project, the Executive Director and at least one emLab Principal Investigator should be able to answer “yes” to the following questions: Is this project right for us? Do we have what we need to be successful? Below are criteria that, if met, would contribute to a “yes” answer for each of the two questions. The number of criteria that have to be met to arrive at a “yes” answer and the threshold for meeting those criteria will shift over time as the interests and priorities of emLab evolve. For example, building long-term priorities, such as a strategic relationship, may be particularly important at times and may lead emLab to take on projects that are less aligned with the core emLab identity or that present greater risks than might otherwise be acceptable. Is this project right for us? These strategic criteria ask whether projects build emLab’s brand and advance its organizational priorities. Aligned with emLab’s mission and research identity. A project must satisfy at least three of the four cornerstones of our research identity (innovative insights, market-based approaches, real-world impact, and collaborative research). emLab projects have the potential to generate new insights and inform durable solutions that generate real-world impact. Projects are deeply innovative and focus on informing and developing sustainable, market-based approaches to pressing environmental issues. Projects have a clear path to real-world impact, often through co-development of research questions and priorities with external stakeholders, who can shape research questions and use research findings to drive change. Strengthens strategic priorities. emLab projects should have a clear potential to strengthen priorities identified by emLab leadership and staff. This includes considerations such as the potential to bring in new datasets or models, strengthen new or existing relationships with partners and funders, or develop emLab’s intellectual capital on priority initiatives and tools. Do we have what we need to be successful? Practical project selection criteria ask whether emLab has the internal capacities and external resources needed to deliver excellent work. In order of importance: PI enthusiasm. Every emLab project is sponsored by an emLab Principal Investigator who is excited to develop, execute, and deliver the project. Adequately resourced. When developing and scoping projects, PIs should ensure that the emLab team will have the funding and timeline needed to deliver the project. They can additionally make sure the team has access to the datasets and partnerships needed to deliver the project and facilitate successful implementation. Staff capacity. emLab takes on new projects if (1) we have research staff with availability and required expertise or (2) we are confident we can recruit the expertise and capacity to fit the needs of the project. 7.2 Setting projects up for success in project scoping As a project is scoped, the PI and emLab operations team should clearly define project objectives/research questions, scope, approach, timeline and capacity needs. Key considerations in this process include: Follow emLab project selection criteria to evaluate project fit (novel insights, uniquely qualified, strengthen strategic priorities) and capacity to deliver (PI enthusiasm and ownership, staff capacities and skill sets, adequately resourced), and identify potential risks Clarify and align on expectations with partners/sponsor on budget, SOW, methods and approaches, data needs, timelines, their objectives and end goals for the research, and how much flexibility there is around specific deliverables outlined in the SOW. Identify the capacity needs and team composition including level of project management and communications support, project scientists, postdoctoral researchers, and graduate and undergraduate student researchers. "], -["emlab-workflow-and-platforms.html", "Section 8 emLab workflow and platforms 8.1 Email 8.2 Calendar 8.3 Zoom 8.4 Slack 8.5 Google Shared Drive 8.6 Nextcloud and the emLab server 8.7 Git and GitHub 8.8 Zotero 8.9 Project management platforms 8.10 Data and code standard operating procedure", " Section 8 emLab workflow and platforms To support both organization and collaboration, a standardized, transparent, and version controlled workflow is central to our team. We rely on the Google Suite (e.g., Gmail, Google Drive, Google Calendar), Slack, and Zoom to centralize and facilitate internal and external communication, and GitHub, Zotero, Shared Drive, and Nextcloud/the emLab server to support our data science and other project-related work. The sections below detail how we use each of these platforms and how to set them up. We have separate documentation for our data and code standard operating procedures. 8.1 Email Coming soon 8.2 Calendar Our team relies heavily on Google Calendar to check team members’ availability and schedule meetings. Please keep your calendar up to date! Setting out of office notifications The best way to let people know if you are on vacation or out of the office is by setting up your calendar event as “Out of Office” instead of a regular event. You can customize this to automatically decline meetings on that day. Adding other calendars To view team member’s calendars, click on the plus symbol next to “Other calendars” on the left hand side of your calendar and select “Subscribe to calendar.” There is a full list of team emails in the emLab Team Roster document. Scheduling rooms See Chapter 13.1 for information on reserving conference rooms. 8.3 Zoom Through UCSB, we have access to a paid Zoom account, which we use for all video conferencing. You can schedule a Zoom meeting (or recurring meetings) through your browser or the Zoom app. Below are our Zoom best practices and guidelines. 8.3.1 Making scheduling easier To make scheduling with Zoom easier, install Zoom for GSuite. Once synced with your Zoom account, it will show up as an option along with Hangouts under conferencing when you create a calendar invite. Once created, you will also be able to see the meeting on your Zoom account. 8.3.2 Being an effective communicator on Zoom Here are a couple of tips for getting the most out of virtual meetings: Everyone on video: it’s nice to see everyone’s face instead of talking to black boxes. If your internet isn’t acting up, turn your video on to have a more engaging conversation. Sharing screens: to keep everyone on the same page, have the presenter share their screen so all of the participants are looking at the same information to avoid any possible confusion. This is a good way to troubleshoot code, walk through documents, etc. The new Zoom default is to only allow the host to screen share. To allow all participants to share their screens, go to your settings and under “who can share?” select “all participants.” Note: If you aren’t comfortable changing this setting, instead turn on the ability to have co-hosts and in the meeting select the screen-sharers to be co-hosts. Whiteboard: Zoom has a whiteboard feature that allows you to draw on your screen for everyone to see. To use this feature, share your screen and select “whiteboard” instead of a browser window. Nonverbal communication: use the reactions feature in the bottom bar of your zoom meeting to react during a meeting. You can also raise your hand in the meeting to signal that you have a question. To raise your hand, open the participant panel by clicking on participants in the lower bar and then click “raise hand” in the lower right hand corner (note: the host can’t raise their hand). Making the most of virtual meetings: Circulate as much as possible (agenda, slides, google docs, etc.) before the meeting so people have time to read/review them If needed, schedule longer meetings to avoid feeling rushed and allow time to repeat things or deal with technical difficulties Notify people ASAP if they are cutting out Dial-in and use phone for audio if your internet connection is poor Turn off videos if connection is poor 8.4 Slack Our team uses Slack on a daily basis to keep communication channels open within teams and across our different offices. We have an emLab workspace that houses all of our channels. When you are first added to Slack, you will be added to the general, random, communications, report and publications, and code channels. Feel free to browse and join other channels in our workspace. You will be added to project specific channels on an as needed basis. You can view Slack either through a broswer window or by downloading the desktop app. 8.4.1 Slack basics Slack is organized into channels and direct messages. Channels are a way to organize conversations and other than a couple general emLab channels, are often project specific. Whatever you share in a channel is viewable by all members of that channel. You can also send direct messages to an individual or a group of up to 9 people. The status feature is helpful for letting others know if you are in a meeting or on vacation, and therefore may not be responding in a timely manner. One great thing about Slack is that it’s searchable. You can search either by person or keywords to find old messages. Additionally, if someone sends you something you will need to reference multiple times, you can save messages by clicking on the bookmark icon on the top right hand corner of the slack and view them by selecting “saved items” in the left menu bar on Slack. You can also mark messages as unread or be reminded about them later by clicking on the 3 vertical dots on a message and selecting “mark unread” or “remind me about this.” People have differing notification preferences, which you can set under Preferences → Notifications. If someone sends you a direct message or tags you, a number will show up on your slack app. If they add something to a channel you are on but don’t tag you, a red dot will show up. To ensure someone gets a numbered notification, either tag them (i.e. @Erin) or tag the channel (i.e. @channel). Tagging the channel will send a notification to every member of that channel. 8.4.2 Creating a channel When a new project starts, create a slack channel for it and add the relevant team members to it. To create a channel, simply click on the plus symbol next to channels and fill out the channel information (Name, Purpose, and Send invites to). If you need to add any guests to a channel, slack Erin with the guest’s email and the channel they need to be added to. 8.5 Google Shared Drive We have all experienced the moment where we can’t remember where a Google Doc is. To help solve this problem, we created an emLab Shared Google Drive, which is a centralized space for all of our Google-related documents to live within a shared file structure. Unlike files in My Drive (your personal Google Drive account), files within the Shared Drive belong to the team instead of an individual. So even if people leave, the files stay exactly where they are and aren’t lost with that person’s account. The structure of Shared Drive is detailed in Section 2. You can read more about Shared Drives here. Please do your best to centralize all of your non-data project documents within the Shared Drive. 8.5.1 Shared Drive structure The emLab Shared Drive is organized into three main folders: central-emlab-resources: includes meeting and event information, onboarding materials, information about travel reimbursements, and the team roster communications: includes the blog schedule, presentation templates, and publication and media tracking. Note: Adobe design projects, photo repository, and emLab logos live on the server. projects: includes information on past and current projects, and project management guidelines A full table of contents can be seen here. 8.5.2 Sharing files There are multiple levels of access people can have to the Shared Drive: member level (i.e. has access to everything within the Shared Drive), folder level, and file level. Members of the Shared Drive can see all folders and files within the Drive. If you want to send a quick link to someone who is part of the Shared Drive, simply copy the URL from your browser. There is no need to create a shared link if you are sending it to someone with access to the emLab Shared Drive. Sharing files and folders with external people works the same as a regular Google Drive folder or file. Simply select “Share” and either add people’s emails or create a shared link. 8.5.3 Shared Drive permissions All full time staff (PIs, postdocs, project researchers, ops) will be added as members of the Shared Drive. Students and collaborators will be added at the folder level for those projects they are engaged in. They can either be directly added to the folder or given a shareable link for access. Note: some institutions are Outlook based and there may be restrictions in adding their university emails to Shared Drive. 8.5.4 Linking the Shared Drive and your Computer 8.5.4.1 Why install Drive for Desktop? As explained above, using a Shared Drive means that individuals don’t “own” the files. All files are instead owned by the emLab Shared Drive, which lives “on the cloud.” You can access these files through a web browser, just as you would access them on Google Drive. However, it is nice to have the files directly in your computer. To do so, you’ll need to install Drive for Desktop, Google’s new system that will partially replace Google Backup and Sync. There are important distinctions between Backup and Sync and Drive for Desktop (previously referred to as Drive File Stream). As the names indicate, Backup and Sync syncs and stores Drive content locally on your computer (that is, it takes up space in your hard drive). Drive for Desktop, however, streams all files and folders from the cloud. You can think of these as owning a DVD vs. streaming the movie from Netflix. You can read more on the differences between these approaches here. 8.5.4.2 Step-by-step installation Step 1: go to Get started with Drive File Stream and select the appropriate installer for your operating system. Note: Make sure you are on your UCSB google account when installing. Step 2: follow the instructions on the install window (you can accept all defaults). Step 3: once the installation is complete, you’ll need to sign in to your account. To do so: Click on the Drive File Stream icon () On Windows machines, it should be on the bottom right corner of your screen On MacOS, it should be at the top right of your screen Sign in with your UCSB account, click through the application overview slides, and finally click on the button to open your Google Drive folder. Once that finder / explorer opens, you should be able to see two folders: 1) My Drive and 2) Shared drives. The first folder will contain files owned by you (that is, your normal Google Drive Files stored on your UCSB account). The second folder will contain all shared drives you are part of. By navigating to that folder, you should see the emLab shared drive, containing all the folders mentioned earlier. 8.5.5 Other considerations 8.5.5.1 Actual location of the Google Drive folder on my computer Remember that Drive for Desktop will stream, not save files to your computer. Therefore, there will be no folder directly under your devices / hard drives. Instead, your computer will detect the Google Drive folder as if it were an external device connected to your machine. On a Mac, the folder will therefore appear on your desktop, or under the Devices tab of your Finder. On a Windows machine, it will appear under This PC, next to your hard drive and any other connected devices. 8.5.5.2 I also want to link a personal gmail account The easiest way to do this is to share the folders from your personal drive that you want access to with your @ucsb.edu email. This avoids the hassle and potential issues that arise by also installing Backup and Sync. 8.6 Nextcloud and the emLab server Everything that is not Google docs/sheets/slides lives on the emLab server, which is managed by GRIT. This includes data files, PDFs, photos, videos, etc. The emLab server can be accessed via a platform called Nextcloud, which is very similar to GoogleDrive where there is a browser option and a desktop app. Below are instructions for signing up for a GRIT account and setting up Nextcloud on your local machine. 8.6.1 Signing up for an account with GRIT If you do not yet have a GRIT account Fill out the GRIT compute access request form (CARF): Under “Faculty” put: Christopher Costello Under “Research Group Name” put: emLab Under “GRIT Server or Service that the person will need access to?” put: emLab group membership (for accessing emLab data storage space and emLab computational servers, including quebracho and sequoia) and Nextcloud group membership. Note: If you are a member of the Waitt team in addition to the above add: emLab Waitt group membership You should receive an email from GRIT saying that your account has been created. Follow any additional instructions provided by GRIT. Create your GRIT access credentials at the following link: . The username and password you use here will be the same username and password for accessing the Nextcloud data directories and emLab servers. If you already have a GRIT account but are not connected to the emLab group Send a help ticket email to GRIT (help@grit.ucsb.edu). Say that you are part of the emLab research group, which has Christopher Costello as the faculty PI. Ask them to please connect the email to the emLab group membership (for accessing emLab data storage space and emLab computational servers, including quebracho and sequoia) and Nextcloud group membership. Follow any additional instructions provided by GRIT. Create your GRIT access credentials at the following link: . The username and password you use here will be the same username and password for accessing the Nextcloud data directories and emLab servers. If you ever need to reset your password, you can use the following link: . 8.6.2 Setting up Nextcloud on your local machine Installation steps for Mac and Linux (note that after Step 2, we only provide screenshots for Mac, but that the Linux experience should look very similar). 8.6.2.1 Downloading the Nextcloud desktop app and connecting it to GRIT Step 1: Download and install the Nextcloud Desktop app. - Linux users: Nextcloud Desktop client packages are also available via the package manager directly for many Linux distributions. Ubuntu and derivative users can get the latest stable release by adding the PPA and then installing via the Software Manager. Step 2: Open the app and click “Log in” mac screenshot Step 3: When prompted, enter https://nextcloud.grit.ucsb.edu as the server address. Step 4: Sign in with your GRIT credentials (created in the section above). It will have you sign in through your browser to grant the Nextcloud desktop app the necessary permissions. Follow the prompts in your browser. 8.6.2.2 Configuring how the Nextcloud desktop app will sync or stream files to your local machine There are generally three approaches for syncing and streaming files to your local machine using the Nextcloud desktop app. We will provide instructions for each of these 3 approaches so that individuals can choose what works best for them. Generally though, we recommend option #3. Option 1: “Stream” the entire emLab directory using virtual files. Pros Virtual files operate similarly to “streaming” using the Google Drive app. Virtual files take up very little hard drive space on your local machine, and are rather just a pointer to the actual file, which is stored on GRIT. You will be able to view the full emLab directory structure on your local machine. The entire contents of the emLab directory will always be available and up-to-date. Cons Virtual files have a .nextcloud extension, since they are just a pointer file. This means for instance that they cannot be directly read into R. To open a virtual file on your local machine, you need to first double-click on it (or right-click on it and say “Make always available locally”). Once you’ve done this, the virtual file is now available on your local machine, but it also now takes up hard drive space. Option 2: Selectively “sync” only a subset of directories. Using this approach, each individual manually selects which directories they want to sync to their local machine. For example, you may choose to only sync the project directories you are actively working with. The emLab Nextcloud directory is very large (multiple TB), so you do not want to do a full sync of the entire emLab directory on your local machine. Pros You will only see the most relevant directories on your local machine. You have complete control over what gets synced onto your local machine. Since files exist on your local machine, you will be able to read/write data exactly as you would with a regular directory on your computer. For example, interacting with data in R would work exactly like it does in other directories on your machine. Synced directories will be available offline without internet access. Cons Synced directories will take up space on your local machine. Since many of our directories are quite large, you will need to ensure you have sufficient hard drive space to sync the directories you want. You will not be able to view the full emLab directory structure on your local machine. However, you can always view the entire directory structure using the Nextcloud browser interface: Whenever you join projects or leave projects, you will need to manually selectively sync directories onto your local machine as needed. So this will require some level of continual effort to ensure the right directories and files are synced. Option 3: “Stream” the entire emLab directory using virtual files, while also syncing a subset of the most relevant directories to be available locally. We imagine that for most people, this will combine the most important pros and avoid the most painful cons from the above two approaches. Additionally, since many researchers will be performing computation on one of the emLab servers, it may be less necessary to sync data files onto your local machine. 8.6.2.2.1 File option 1: Streaming entire emLab directory using virtual files Step 1: After logging in, you will be brought back to the Nextcloud app. Click “Skip folders configuration”. We will set up the necessary connections in a minute. This is important! The emLab Nextcloud directory is very large (multiple TB), so you do not want to do a full sync of the entire directory on your local machine. Step 2: Before continuing, you now need to to set up virtual file support for your local machine, follow these instructions, which vary by system. Mac: navigate to the folder ~/Library/Preferences/Nextcloud. You can do this through the Finder, but a faster way to do this is as follows: Copy and paste this directory path. Open the Spotlight Search, either by pressing command-space or by clicking on the magnifying glass in the upper right-hand corner of your screen. Paste the directory path into the box, then double-click “Nextcloud” to navigate to the directory. Right-click on the file nextcloud.cfg, click “Open with”, then click “TextEdit”. This will now open the configuration file which you will need to edit. Add the following line under the [General] header: showExperimentalOptions=true (you can simply copy and paste the text into the document, like a regular text editor) Finally, save the document (File -> Save), and quit (TextEdit -> Quit TextEdit). Linux Navigate to the directory ~home/your_username/.config/Nextcloud (where your your_username is your individual personal user name) Open the file nextcloud.cfg with a text editor Add the following line under the [General] header: showExperimentalOptions=true Save the file and quit your text editor Step 3: Go back to the Nextcloud app. Click on your name in the app in the upper-right-hand (upper-left for Linux) corner of your desktop, click on your name, and then click Settings. Step 4: Click “Add folder sync connection” Step 5: If you use a Mac, enter /Users/Shared/nextcloud as the folder. This will ensure that the path is the same across most users, and thus all code should work across emLab users. Linux users do not have access to a Shared directory, so will need to use a different path such as /home/your_username/Nextcloud, where your_username is your Linux system user name. Click continue. Step 6: When prompted to select the remote destination folder, select the highest level directory called Nextcloud. The path name should simply show a forward slash, /. Click continue. Step 7: Enable the checkbox option “Use virtual files instead of downloading content immediately (experimental)”. This is important! The emLab Nextcloud directory is very large (multiple TB), so you do not want to do a full sync of the entire directory on your local machine. Virtual files are Nextcloud’s equivalent to the Google Drive concept of streaming. You will be able to see files and directory structures on your local machine, but the files will not take up space on your local machine. Click “Add Sync Connection”, and click that you acknowledge this feature is experimental. Step 8: Everything should now be set up correctly! When you navigate to settings now, you should see something like this. Note that it says “Virtual file support is enabled”. 8.6.2.2.2 File option 2: Syncing a subset of directories Step 1: After logging in, you will be brought back to the Nextcloud app. Click “Choose what to sync”. This will bring you to a screen that contains all emLab directories. You may now select the subset of directories you wish to sync. Click “Add Sync Connection” after you have selected the appropriate directories. Step 2: After completing the setup process, you can always add more directories to sync later on, or can always remove synced directories. To add new directories you want to sync: in the Nextcloud app, simply right-click on the directory you want to sync locally, click “Availability”, and click “Make always available locally”. To remove synced directories, you can instead click “Free up local space”. 8.6.2.2.3 File option 3: Streaming entire emLab directory using virtual files, and syncing a subset of directories Step 1: First, follow the instructions above for streaming the entire emLab directory using virtual files (option 1). Step 2: Next, sync the directories you want to be made available locally. By default, all directories and files will be virtual. However, you may wish to have some directories stored locally on your computer, for example to ensure that you can access them when you are offline. You can enable this on a case-by-case basis for specific directories. Just note that some directories are very large, and by doing this, the files in that directory will take up space on your local computer. As an example, here’s how to do this for the test-project-nextcloud directory. In the Nextcloud app, simply right-click on the directory you want to sync locally, click “Availability”, and click “Make always available locally”: Alternatively, you can also do this on a Mac in your finder. Navigate to the directory you want to sync, right click on it, click “Nextcloud” and then click “Make always available locally”. If you just want to sync a single file, you can also download virtual files, which have .nextcloud on the end of the filename, from your normal file finder by double clicking on them. They should then automatically download and open in the default app for that file type. Note that when you do this, the .nextcloud extension will disappear, and only the regular file extension will remain. This will also make these files available offline. 8.6.2.3 Making sure everything worked You should also now be able to see the Nextcloud directory in your finder. Note that this will take some time to populate as the virtual files are set up. On a Mac, you should be able to navigate to Nextcloud on your finder directly. You can always simply navigate to the directory as well, /Users/Shared/nextcloud. 8.7 Git and GitHub Since most of our projects at emLab involve code, we use Git to track changes made to our code and facilitate collaboration by merging changes made by others, and GitHub to organize, share, and backup our code. This section provides a brief overview of how Git and GitHub work, how to install them on your computer (and how to join the emLab GitHub page), and some general guidelines for how to use GitHub to organize code associated with emLab projects. 8.7.1 What are Git and GitHub? Git is an open-source version control system designed for programmers. Git can operate as a standalone program on your computer, but can also be operated through many other programs (or “clients”). GitHub (really github.com) is a hosting service that provides online storage for your Git-projects. Think of Git as a little creature that keeps a record of all of the changes made to a file stored on your computer, and GitHub as a safe place on the internet that the little creature can go and put a copy of that file (and the changes you’ve made) when you tell it to do so. There are a number of good tutorials with more information on how Git and GitHub work (as well as how you can set them up to sync directly through other programs such as RStudio). The Ocean Health Index team at the National Center for Ecological Analysis and Synthesis (NCEAS) here in Santa Barbara created a very detailed data science training that includes two excellent tutorials on setting up and collaborating with GitHub: GitHub Collaborating with GitHub If you’re new to using Git and GitHub, the two tutorials listed above are a great place to start since NCEAS and emLab often operate in a similar way. Additionally, see the Software Carpentry’s lesson for the Git novice. If you primarily use (or will use) R for coding, Jenny Bryan also has an excellent tutorial specifically about how to integrate Git and GitHub with R: Happy Git and GitHub for the useR If you’re interested in learning more about all of the functionality GitHub has to offer, the Openscapes team at NCEAS has also tutorials on how to use GitHub for publishing code and for project management: GitHub for Publishing GitHub for Project Management 8.7.2 Helpful terminology Git and GitHub use some weird terms that might be unfamiliar. Before installing and setting up Git and GitHub, here are a few key terms you may come across: repository (“repo”): a collection of files pertaining to the same project, document, goal, etc. Generally there’s a single repository for each project at emLab containing all of the code associated with that project. This repository can be organized with multiple folders and subfolders. commit: a set of changes made by a user to one or more files in a repository that the user wants to prepare to send to GitHub. push: the action of sending a commit from your local machine to the remote GitHub directory. pull: the action of retrieving any commits that have been made to the repository and are stored in the remote GitHub directory but are NOT on your local machine. 8.7.3 How to install Git and GitHub Most of tutorials listed above include detailed instructions on how to install Git and GitHub. The short version (and steps specific to getting incorporated with the emLab GitHub page) are listed below. For more detailed instructions, please refer to the tutorials listed above. Step 1: Create a free GitHub account Notes: use your @ucsb.edu email make sure you remember your username and password, you’ll need this later Since GitHub is a company, and is used by many different types of organizations in many different industries, they offer a few different pricing schemes/deals. As an individual, once you create a username and sign up for an account, you get an unlimited number of free public and private repositories, but the number of external collaborators allowed in private repositories is limited to three. GitHub also offers a “Pro” plan for $7/month giving you unlimited external collaborators on all of your private repositories. However, for students, faculty, and research staff, or official nonprofit organizations and charities GitHub waives this fee through its GitHub Education and GitHub for Good programs. Good news! emLab qualifies as an educational organization through the GitHub Education program, and as a UCSB staff member you qualify for the individual educational discount. So, once you’ve signed up for a free account on GitHub… Step 2: Register as a researcher Go to the GitHub Education page and register as a researcher Note: this is why you should use your @ucsb.edu email for step 1. Click on the “Get benefits” link in the top right-hand corner and follow the directions to upgrade your account to a “Pro” account for free. You may need to take a picture of your UCSB ID card to submit as part of this process. GitHub may also periodically ask you to re-verify your eligability to qualify for this program. Step 3: Get invited to the emLab GitHub organization Send Erin O’Reilly a Slack message (or an email if you must… eoreilly@ucsb.edu) with your new GitHub username so you can be added to the emLab GitHub page! The emLab GitHub page is where the repositories for all emLab projects live (more on this later), and once you are a member of the organization you will be able to create new public and private repositories that appear here (as well as on your personal page). Step 4: Install Git If you’re very very lucky, Git will already be installed on your computer. Open the shell for your opperating system. If you’re using Mac OS X, this is called Terminal. If you’re using Windows, you have multiple types of shells, but you should be using a Git Bash shell (NOT Power Shell). The easiest way to find out whether Git is already installed on your machine is to type the following: git --version ## git version 2.20.1 (Apple Git-117) If it returns a version number, you already have Git installed! However, if it returns something like git: command not found, you need to install Git. There are a number of different ways to install Git. Stand-alone installers exist for Mac OS X and Windows. If you’re using Linux, you probably already know how to install Git. If you’re using Mac OS X, Git can also be installed as part of the XCode Command Line tools, or you can also install it using Homebrew. If you’re interested in either of those options, follow the cooresponding directions in Jenny Bryan’s tutorial. If that sentence doesn’t mean anything to you, download the installer from the link above and follow the prompts. Once you’ve installed Git via whichever method you’ve chosen for your operating system, open the shell again and retype the same command to verify that the installation was successful: git --version ## git version 2.20.1 (Apple Git-117) It should now return a version number. Step 5: Tell Git who you are Git needs to know a little bit more about you in order to play nicely. In particular there are two things that it’s helpful to configure: 1) The name that will be associated with any commits you make, and 2) the email address asssociated with your GitHub account. To set these two things, type the following into the shell using your name and email: git config --global user.name 'Jane Doe' git config --global user.email 'jane@example.com' The user name input here should be your full name (i.e. it does not need to be the same as your username for GitHub), but the email DOES need to be the same as that associated with your GitHub account. You can then check to make sure these were entered correctly by typing: git config --global --list Step 6 (optional): Store your credentials (so you don’t have to type your password every time) Git will sometimes want to make sure you are you when performing certain operations. For example, when cloning a private repo or when you want to push changes to a repo. If you don’t want to do this every time, you can tell Git to remember your password too. You can read more about Git’s credential management here. On your terminal, navigate to a repository on your computer. (You can also use the Terminal pane within RStudio) and type the following into the shell: # Tell git to use the credential.helper git config --global credential.helper store # git pull (or git push) will prompt you to enter your password git pull What we just did was to tell Git to store our credentials. So, after typing them this one time, you should not need to type it again. Step 7 (optional): Install a client for Git to make your life easier If you actually tried step 6 and you’re still reading this, you probably don’t usually spend a lot of time running commands in the shell and the last step didn’t make a lot of sense. If that’s the case, you might want to also install a Git client in order to help you visualize what Git is actually doing. You do not need a Git client to take advantage of version-control functionality of Git, as everything can be done using the shell (as in the previous step). However, the shell is not user-friendly. There are a number of Git/GitHub clients that you can download to interact with Git and GitHub in a more visual way. If you use RStudio, there is a very basic Git client built in that may be enough to get you started (more on this later). Other nice free Git clients include: GitKraken (available for all platforms, plus the logo octopus is pretty sweet…) GitFiend (cross-platform) SourceTree (has some problems on Mac OS X) GitHub Desktop (not available for Linux) GitUp (only for Mac OS X) There are many more. See Jenny Bryan’s tutorial if you’re not satisfied with those choices. Once you’ve installed a Git client, follow the directions to connect to your GitHub account. Once you’ve done this, try opening the local version of the repository you made in step 6, and notice the nice visual representation of the changes you made. 8.7.4 General guidelines for using GitHub at emLab In general, each emLab project should have its own repository. There may be some cases in which multiple repositories may be associated with the same project, but this should be avoided if possible. The project repository should be created within the emLab GitHub page (exceptions may exist for example if a partner organization requires that the project repository be created within their organization’s GitHub page). Repositories can be made public or private when they are created (depending on the nature of the project) while the project is ongoing, but should be made public when the project is complete. Since many previous (and ongoing) projects were created within the personal GitHub pages of emLab members, the ownership of these repositories should be transferred to the emLab GitHub page at the conclusion of the project if possible. In order to ensure that the relevant researchers are notified of issues and other activities, researchers should “watch” or “subscribe” to repositories in which they work. 8.8 Zotero emLab uses Zotero to collaboratively collect, organize, and cite publications. We organize publications into Group Libraries which can be at the project or paper level. Our account – emlab-ucsb – has unlimited storage and there is no limit to the number of people you can add to a library. In Zotero, storage for a library only counts against the owner, so the emLab account must be the owner of the library for access to unlimited storage. 8.8.1 Making emLab the owner of a library If creating a new group library, slack/email Erin (eoreilly@ucsb.edu) and she can directly create the library under the emLab account. If you are the owner of an existing library and would like to transfer ownership to emLab, first invite emlab-ucsb to be a member of the library. Once that invitation has been accepted, then go to “Group Settings” for the library and in the bottom right of the page, select transfer ownership to the emLab account. 8.8.2 Saving publications to a library To use Zotero properly, you need to install the Zotero Connector for your browser in addition to the Zotero desktop app (see this page for downloads). The most convenient way to save publications to Zotero is through Zotero Connector. The Zotero Connector allows you to add publications from your browser to Zotero with a single click. The “save” button shows up in the upper right corner of your browser and the symbol appears differently depending on the type of reference you are viewing (e.g. book, PDF, webpage). After you click the save button, a popup will appear that allows you to select the library to save the reference to. Read more about saving items to Zotero here. 8.8.3 Zotero integration with GoogleDocs and Word Zotero is a great resource for adding references to a manuscript. It is integrated into both Word and GoogleDocs for easy use. As a note, you have to take extra steps to ensure that your references remain linked when switching between Word and GoogleDocs. See this document for more information about moving documents with Zotero citations between word processors. 8.8.3.1 Adding a citation to your document In both Word and GoogleDocs, Zotero shows up as a separate tab/menu item for you to choose from. For example, this is the Zotero tab in Word. To add an in-text citation, place your cursor after the statement you want to reference and then click on “Add/Edit Citation.” This brings up a Zotero search bar that allows you to search for a reference within your libraries based on a keyword or author. As you type, Zotero brings up options that you can select from. Once you select the citation, either insert a comma to add another citation or select enter to add the reference. Note: If you are adding a citation for the first time to a document, you will be asked to select the citation style. This allows you to add a reference style based on your target journal. 8.8.3.2 Adding a bibliography to your document The most amazing thing about Zotero is that it automatically generates a bibliography for you based on your in-text citations. To add a bibliography, simply place your cursor where you want to add your reference list and select “Add/Edit Bibliography.” It will add all of the references for you based on the citation style selected. 8.9 Project management platforms There are many available cloud-based project management tools and platforms to help facilitate project management and track milestones and deliverables. It is up to each project manager and team to select a system that works best for their individual project and the team. See project execution section for more details and emLab templates for work planning. 8.10 Data and code standard operating procedure Since we love GitHub and open data science, we have a whole Bookdown dedicated to data and code standard operating procedures for emLab. In this document, you will find information about data storage, metadata, tidy data, code style guides, code reproducibility, high performance computing, and more. This is a living document, so please feel free to suggest updates in the data-streamlining slack channel. "], +["emlab-workflow-and-platforms.html", "Section 8 emLab workflow and platforms 8.1 Email 8.2 Calendar 8.3 Zoom 8.4 Slack 8.5 Google Shared Drive 8.6 Nextcloud and the emLab server 8.7 Git and GitHub 8.8 Zotero 8.9 Project management platforms 8.10 Data and code standard operating procedure", " Section 8 emLab workflow and platforms To support both organization and collaboration, a standardized, transparent, and version controlled workflow is central to our team. We rely on the Google Suite (e.g., Gmail, Google Drive, Google Calendar), Slack, and Zoom to centralize and facilitate internal and external communication, and GitHub, Zotero, Shared Drive, and Nextcloud/the emLab server to support our data science and other project-related work. The sections below detail how we use each of these platforms and how to set them up. We have separate documentation for our data and code standard operating procedures. 8.1 Email Coming soon 8.2 Calendar Our team relies heavily on Google Calendar to check team members’ availability and schedule meetings. Please keep your calendar up to date! Setting out of office notifications The best way to let people know if you are on vacation or out of the office is by setting up your calendar event as “Out of Office” instead of a regular event. You can customize this to automatically decline meetings on that day. Adding other calendars To view team member’s calendars, click on the plus symbol next to “Other calendars” on the left hand side of your calendar and select “Subscribe to calendar.” There is a full list of team emails in the emLab Team Roster document. Scheduling rooms See Chapter 13.1 for information on reserving conference rooms. 8.3 Zoom Through UCSB, we have access to a paid Zoom account, which we use for all video conferencing. You can schedule a Zoom meeting (or recurring meetings) through your browser or the Zoom app. Below are our Zoom best practices and guidelines. 8.3.1 Making scheduling easier To make scheduling with Zoom easier, install Zoom for GSuite. Once synced with your Zoom account, it will show up as an option along with Hangouts under conferencing when you create a calendar invite. Once created, you will also be able to see the meeting on your Zoom account. 8.3.2 Being an effective communicator on Zoom Here are a couple of tips for getting the most out of virtual meetings: Everyone on video: it’s nice to see everyone’s face instead of talking to black boxes. If your internet isn’t acting up, turn your video on to have a more engaging conversation. Sharing screens: to keep everyone on the same page, have the presenter share their screen so all of the participants are looking at the same information to avoid any possible confusion. This is a good way to troubleshoot code, walk through documents, etc. The new Zoom default is to only allow the host to screen share. To allow all participants to share their screens, go to your settings and under “who can share?” select “all participants.” Note: If you aren’t comfortable changing this setting, instead turn on the ability to have co-hosts and in the meeting select the screen-sharers to be co-hosts. Whiteboard: Zoom has a whiteboard feature that allows you to draw on your screen for everyone to see. To use this feature, share your screen and select “whiteboard” instead of a browser window. Nonverbal communication: use the reactions feature in the bottom bar of your zoom meeting to react during a meeting. You can also raise your hand in the meeting to signal that you have a question. To raise your hand, open the participant panel by clicking on participants in the lower bar and then click “raise hand” in the lower right hand corner (note: the host can’t raise their hand). Making the most of virtual meetings: Circulate as much as possible (agenda, slides, google docs, etc.) before the meeting so people have time to read/review them If needed, schedule longer meetings to avoid feeling rushed and allow time to repeat things or deal with technical difficulties Notify people ASAP if they are cutting out Dial-in and use phone for audio if your internet connection is poor Turn off videos if connection is poor 8.4 Slack Our team uses Slack on a daily basis to keep communication channels open within teams and across our different offices. We have an emLab workspace that houses all of our channels. When you are first added to Slack, you will be added to the general, random, communications, report and publications, and code channels. Feel free to browse and join other channels in our workspace. You will be added to project specific channels on an as needed basis. You can view Slack either through a broswer window or by downloading the desktop app. 8.4.1 Slack basics Slack is organized into channels and direct messages. Channels are a way to organize conversations and other than a couple general emLab channels, are often project specific. Whatever you share in a channel is viewable by all members of that channel. You can also send direct messages to an individual or a group of up to 9 people. The status feature is helpful for letting others know if you are in a meeting or on vacation, and therefore may not be responding in a timely manner. One great thing about Slack is that it’s searchable. You can search either by person or keywords to find old messages. Additionally, if someone sends you something you will need to reference multiple times, you can save messages by clicking on the bookmark icon on the top right hand corner of the slack and view them by selecting “saved items” in the left menu bar on Slack. You can also mark messages as unread or be reminded about them later by clicking on the 3 vertical dots on a message and selecting “mark unread” or “remind me about this.” People have differing notification preferences, which you can set under Preferences → Notifications. If someone sends you a direct message or tags you, a number will show up on your slack app. If they add something to a channel you are on but don’t tag you, a red dot will show up. To ensure someone gets a numbered notification, either tag them (i.e. @Erin) or tag the channel (i.e. @channel). Tagging the channel will send a notification to every member of that channel. 8.4.2 Creating a channel When a new project starts, create a slack channel for it and add the relevant team members to it. To create a channel, simply click on the plus symbol next to channels and fill out the channel information (Name, Purpose, and Send invites to). If you need to add any guests to a channel, slack Erin with the guest’s email and the channel they need to be added to. 8.5 Google Shared Drive We have all experienced the moment where we can’t remember where a Google Doc is. To help solve this problem, we created an emLab Shared Google Drive, which is a centralized space for all of our Google-related documents to live within a shared file structure. Unlike files in My Drive (your personal Google Drive account), files within the Shared Drive belong to the team instead of an individual. So even if people leave, the files stay exactly where they are and aren’t lost with that person’s account. The structure of Shared Drive is detailed in Section 2. You can read more about Shared Drives here. Please do your best to centralize all of your non-data project documents within the Shared Drive. 8.5.1 Shared Drive structure The emLab Shared Drive is organized into three main folders: central-emlab-resources: includes meeting and event information, onboarding materials, information about travel reimbursements, and the team roster communications: includes the blog schedule, presentation templates, and publication and media tracking. Note: Adobe design projects, photo repository, and emLab logos live on the server. projects: includes information on past and current projects, and project management guidelines A full table of contents can be seen here. 8.5.2 Sharing files There are multiple levels of access people can have to the Shared Drive: member level (i.e. has access to everything within the Shared Drive), folder level, and file level. Members of the Shared Drive can see all folders and files within the Drive. If you want to send a quick link to someone who is part of the Shared Drive, simply copy the URL from your browser. There is no need to create a shared link if you are sending it to someone with access to the emLab Shared Drive. Sharing files and folders with external people works the same as a regular Google Drive folder or file. Simply select “Share” and either add people’s emails or create a shared link. 8.5.3 Shared Drive permissions All full time staff (PIs, postdocs, project researchers, ops) will be added as members of the Shared Drive. Students and collaborators will be added at the folder level for those projects they are engaged in. They can either be directly added to the folder or given a shareable link for access. Note: some institutions are Outlook based and there may be restrictions in adding their university emails to Shared Drive. 8.5.4 Linking the Shared Drive and your Computer 8.5.4.1 Why install Drive for Desktop? As explained above, using a Shared Drive means that individuals don’t “own” the files. All files are instead owned by the emLab Shared Drive, which lives “on the cloud.” You can access these files through a web browser, just as you would access them on Google Drive. However, it is nice to have the files directly in your computer. To do so, you’ll need to install Drive for Desktop, Google’s new system that will partially replace Google Backup and Sync. There are important distinctions between Backup and Sync and Drive for Desktop (previously referred to as Drive File Stream). As the names indicate, Backup and Sync syncs and stores Drive content locally on your computer (that is, it takes up space in your hard drive). Drive for Desktop, however, streams all files and folders from the cloud. You can think of these as owning a DVD vs. streaming the movie from Netflix. You can read more on the differences between these approaches here. 8.5.4.2 Step-by-step installation Step 1: go to Get started with Drive File Stream and select the appropriate installer for your operating system. Note: Make sure you are on your UCSB google account when installing. Step 2: follow the instructions on the install window (you can accept all defaults). Step 3: once the installation is complete, you’ll need to sign in to your account. To do so: Click on the Drive File Stream icon () On Windows machines, it should be on the bottom right corner of your screen On MacOS, it should be at the top right of your screen Sign in with your UCSB account, click through the application overview slides, and finally click on the button to open your Google Drive folder. Once that finder / explorer opens, you should be able to see two folders: 1) My Drive and 2) Shared drives. The first folder will contain files owned by you (that is, your normal Google Drive Files stored on your UCSB account). The second folder will contain all shared drives you are part of. By navigating to that folder, you should see the emLab shared drive, containing all the folders mentioned earlier. 8.5.5 Other considerations 8.5.5.1 Actual location of the Google Drive folder on my computer Remember that Drive for Desktop will stream, not save files to your computer. Therefore, there will be no folder directly under your devices / hard drives. Instead, your computer will detect the Google Drive folder as if it were an external device connected to your machine. On a Mac, the folder will therefore appear on your desktop, or under the Devices tab of your Finder. On a Windows machine, it will appear under This PC, next to your hard drive and any other connected devices. 8.5.5.2 I also want to link a personal gmail account The easiest way to do this is to share the folders from your personal drive that you want access to with your @ucsb.edu email. This avoids the hassle and potential issues that arise by also installing Backup and Sync. 8.6 Nextcloud and the emLab server Everything that is not Google docs/sheets/slides lives on the emLab server, which is managed by GRIT. This includes data files, PDFs, photos, videos, etc. The emLab server can be accessed via a platform called Nextcloud, which is very similar to GoogleDrive where there is a browser option and a desktop app. Below are instructions for signing up for a GRIT account and setting up Nextcloud on your local machine. 8.6.1 Signing up for an account with GRIT If you do not yet have a GRIT account Fill out the GRIT compute access request form (CARF): https://forms.gle/kqzttgMAjzt867FZA Under “Faculty” put: Christopher Costello Under “Research Group Name” put: emLab Under “GRIT Server or Service that the person will need access to?” put: emLab group membership (for accessing emLab data storage space and emLab computational servers, including quebracho and sequoia) and Nextcloud group membership. Note: If you are a member of the Waitt team in addition to the above add: emLab Waitt group membership You should receive an email from GRIT saying that your account has been created. Follow any additional instructions provided by GRIT. Create your GRIT access credentials at the following link: https://dc1.grit.ucsb.edu/. The username and password you use here will be the same username and password for accessing the Nextcloud data directories and emLab servers. If you already have a GRIT account but are not connected to the emLab group Send a help ticket email to GRIT (help@grit.ucsb.edu). Say that you are part of the emLab research group, which has Christopher Costello as the faculty PI. Ask them to please connect the email to the emLab group membership (for accessing emLab data storage space and emLab computational servers, including quebracho and sequoia) and Nextcloud group membership. Follow any additional instructions provided by GRIT. Create your GRIT access credentials at the following link: https://dc1.grit.ucsb.edu/. The username and password you use here will be the same username and password for accessing the Nextcloud data directories and emLab servers. If you ever need to reset your password, you can use the following link: https://selfservice.grit.ucsb.edu/. 8.6.2 Setting up Nextcloud on your local machine Installation steps for Mac and Linux (note that after Step 2, we only provide screenshots for Mac, but that the Linux experience should look very similar). 8.6.2.1 Downloading the Nextcloud desktop app and connecting it to GRIT Step 1: Download and install the Nextcloud Desktop app. - Linux users: Nextcloud Desktop client packages are also available via the package manager directly for many Linux distributions. Ubuntu and derivative users can get the latest stable release by adding the PPA and then installing via the Software Manager. Step 2: Open the app and click “Log in” mac screenshot Step 3: When prompted, enter https://nextcloud.grit.ucsb.edu as the server address. Step 4: Sign in with your GRIT credentials (created in the section above). It will have you sign in through your browser to grant the Nextcloud desktop app the necessary permissions. Follow the prompts in your browser. 8.6.2.2 Configuring how the Nextcloud desktop app will sync or stream files to your local machine There are generally three approaches for syncing and streaming files to your local machine using the Nextcloud desktop app. We will provide instructions for each of these 3 approaches so that individuals can choose what works best for them. Generally though, we recommend option #3. Option 1: “Stream” the entire emLab directory using virtual files. Pros Virtual files operate similarly to “streaming” using the Google Drive app. Virtual files take up very little hard drive space on your local machine, and are rather just a pointer to the actual file, which is stored on GRIT. You will be able to view the full emLab directory structure on your local machine. The entire contents of the emLab directory will always be available and up-to-date. Cons Virtual files have a .nextcloud extension, since they are just a pointer file. This means for instance that they cannot be directly read into R. To open a virtual file on your local machine, you need to first double-click on it (or right-click on it and say “Make always available locally”). Once you’ve done this, the virtual file is now available on your local machine, but it also now takes up hard drive space. Option 2: Selectively “sync” only a subset of directories. Using this approach, each individual manually selects which directories they want to sync to their local machine. For example, you may choose to only sync the project directories you are actively working with. The emLab Nextcloud directory is very large (multiple TB), so you do not want to do a full sync of the entire emLab directory on your local machine. Pros You will only see the most relevant directories on your local machine. You have complete control over what gets synced onto your local machine. Since files exist on your local machine, you will be able to read/write data exactly as you would with a regular directory on your computer. For example, interacting with data in R would work exactly like it does in other directories on your machine. Synced directories will be available offline without internet access. Cons Synced directories will take up space on your local machine. Since many of our directories are quite large, you will need to ensure you have sufficient hard drive space to sync the directories you want. You will not be able to view the full emLab directory structure on your local machine. However, you can always view the entire directory structure using the Nextcloud browser interface: https://nextcloud.grit.ucsb.edu/index.php/apps/files Whenever you join projects or leave projects, you will need to manually selectively sync directories onto your local machine as needed. So this will require some level of continual effort to ensure the right directories and files are synced. Option 3: “Stream” the entire emLab directory using virtual files, while also syncing a subset of the most relevant directories to be available locally. We imagine that for most people, this will combine the most important pros and avoid the most painful cons from the above two approaches. Additionally, since many researchers will be performing computation on one of the emLab servers, it may be less necessary to sync data files onto your local machine. 8.6.2.2.1 File option 1: Streaming entire emLab directory using virtual files Step 1: After logging in, you will be brought back to the Nextcloud app. Click “Skip folders configuration”. We will set up the necessary connections in a minute. This is important! The emLab Nextcloud directory is very large (multiple TB), so you do not want to do a full sync of the entire directory on your local machine. Step 2: Before continuing, you now need to to set up virtual file support for your local machine, follow these instructions, which vary by system. Mac: navigate to the folder ~/Library/Preferences/Nextcloud. You can do this through the Finder, but a faster way to do this is as follows: Copy and paste this directory path. Open the Spotlight Search, either by pressing command-space or by clicking on the magnifying glass in the upper right-hand corner of your screen. Paste the directory path into the box, then double-click “Nextcloud” to navigate to the directory. Right-click on the file nextcloud.cfg, click “Open with”, then click “TextEdit”. This will now open the configuration file which you will need to edit. Add the following line under the [General] header: showExperimentalOptions=true (you can simply copy and paste the text into the document, like a regular text editor) Finally, save the document (File -> Save), and quit (TextEdit -> Quit TextEdit). Linux Navigate to the directory ~home/your_username/.config/Nextcloud (where your your_username is your individual personal user name) Open the file nextcloud.cfg with a text editor Add the following line under the [General] header: showExperimentalOptions=true Save the file and quit your text editor Step 3: Go back to the Nextcloud app. Click on your name in the app in the upper-right-hand (upper-left for Linux) corner of your desktop, click on your name, and then click Settings. Step 4: Click “Add folder sync connection” Step 5: If you use a Mac, enter /Users/Shared/nextcloud as the folder. This will ensure that the path is the same across most users, and thus all code should work across emLab users. Linux users do not have access to a Shared directory, so will need to use a different path such as /home/your_username/Nextcloud, where your_username is your Linux system user name. Click continue. Step 6: When prompted to select the remote destination folder, select the highest level directory called Nextcloud. The path name should simply show a forward slash, /. Click continue. Step 7: Enable the checkbox option “Use virtual files instead of downloading content immediately (experimental)”. This is important! The emLab Nextcloud directory is very large (multiple TB), so you do not want to do a full sync of the entire directory on your local machine. Virtual files are Nextcloud’s equivalent to the Google Drive concept of streaming. You will be able to see files and directory structures on your local machine, but the files will not take up space on your local machine. Click “Add Sync Connection”, and click that you acknowledge this feature is experimental. Step 8: Everything should now be set up correctly! When you navigate to settings now, you should see something like this. Note that it says “Virtual file support is enabled”. 8.6.2.2.2 File option 2: Syncing a subset of directories Step 1: After logging in, you will be brought back to the Nextcloud app. Click “Choose what to sync”. This will bring you to a screen that contains all emLab directories. You may now select the subset of directories you wish to sync. Click “Add Sync Connection” after you have selected the appropriate directories. Step 2: After completing the setup process, you can always add more directories to sync later on, or can always remove synced directories. To add new directories you want to sync: in the Nextcloud app, simply right-click on the directory you want to sync locally, click “Availability”, and click “Make always available locally”. To remove synced directories, you can instead click “Free up local space”. 8.6.2.2.3 File option 3: Streaming entire emLab directory using virtual files, and syncing a subset of directories Step 1: First, follow the instructions above for streaming the entire emLab directory using virtual files (option 1). Step 2: Next, sync the directories you want to be made available locally. By default, all directories and files will be virtual. However, you may wish to have some directories stored locally on your computer, for example to ensure that you can access them when you are offline. You can enable this on a case-by-case basis for specific directories. Just note that some directories are very large, and by doing this, the files in that directory will take up space on your local computer. As an example, here’s how to do this for the test-project-nextcloud directory. In the Nextcloud app, simply right-click on the directory you want to sync locally, click “Availability”, and click “Make always available locally”: Alternatively, you can also do this on a Mac in your finder. Navigate to the directory you want to sync, right click on it, click “Nextcloud” and then click “Make always available locally”. If you just want to sync a single file, you can also download virtual files, which have .nextcloud on the end of the filename, from your normal file finder by double clicking on them. They should then automatically download and open in the default app for that file type. Note that when you do this, the .nextcloud extension will disappear, and only the regular file extension will remain. This will also make these files available offline. 8.6.2.3 Making sure everything worked You should also now be able to see the Nextcloud directory in your finder. Note that this will take some time to populate as the virtual files are set up. On a Mac, you should be able to navigate to Nextcloud on your finder directly. You can always simply navigate to the directory as well, /Users/Shared/nextcloud. 8.7 Git and GitHub Since most of our projects at emLab involve code, we use Git to track changes made to our code and facilitate collaboration by merging changes made by others, and GitHub to organize, share, and backup our code. This section provides a brief overview of how Git and GitHub work, how to install them on your computer (and how to join the emLab GitHub page), and some general guidelines for how to use GitHub to organize code associated with emLab projects. 8.7.1 What are Git and GitHub? Git is an open-source version control system designed for programmers. Git can operate as a standalone program on your computer, but can also be operated through many other programs (or “clients”). GitHub (really github.com) is a hosting service that provides online storage for your Git-projects. Think of Git as a little creature that keeps a record of all of the changes made to a file stored on your computer, and GitHub as a safe place on the internet that the little creature can go and put a copy of that file (and the changes you’ve made) when you tell it to do so. There are a number of good tutorials with more information on how Git and GitHub work (as well as how you can set them up to sync directly through other programs such as RStudio). The Ocean Health Index team at the National Center for Ecological Analysis and Synthesis (NCEAS) here in Santa Barbara created a very detailed data science training that includes two excellent tutorials on setting up and collaborating with GitHub: GitHub Collaborating with GitHub If you’re new to using Git and GitHub, the two tutorials listed above are a great place to start since NCEAS and emLab often operate in a similar way. Additionally, see the Software Carpentry’s lesson for the Git novice. If you primarily use (or will use) R for coding, Jenny Bryan also has an excellent tutorial specifically about how to integrate Git and GitHub with R: Happy Git and GitHub for the useR If you’re interested in learning more about all of the functionality GitHub has to offer, the Openscapes team at NCEAS has also tutorials on how to use GitHub for publishing code and for project management: GitHub for Publishing GitHub for Project Management 8.7.2 Helpful terminology Git and GitHub use some weird terms that might be unfamiliar. Before installing and setting up Git and GitHub, here are a few key terms you may come across: repository (“repo”): a collection of files pertaining to the same project, document, goal, etc. Generally there’s a single repository for each project at emLab containing all of the code associated with that project. This repository can be organized with multiple folders and subfolders. commit: a set of changes made by a user to one or more files in a repository that the user wants to prepare to send to GitHub. push: the action of sending a commit from your local machine to the remote GitHub directory. pull: the action of retrieving any commits that have been made to the repository and are stored in the remote GitHub directory but are NOT on your local machine. 8.7.3 How to install Git and GitHub Most of tutorials listed above include detailed instructions on how to install Git and GitHub. The short version (and steps specific to getting incorporated with the emLab GitHub page) are listed below. For more detailed instructions, please refer to the tutorials listed above. Step 1: Create a free GitHub account Notes: use your @ucsb.edu email make sure you remember your username and password, you’ll need this later Since GitHub is a company, and is used by many different types of organizations in many different industries, they offer a few different pricing schemes/deals. As an individual, once you create a username and sign up for an account, you get an unlimited number of free public and private repositories, but the number of external collaborators allowed in private repositories is limited to three. GitHub also offers a “Pro” plan for $7/month giving you unlimited external collaborators on all of your private repositories. However, for students, faculty, and research staff, or official nonprofit organizations and charities GitHub waives this fee through its GitHub Education and GitHub for Good programs. Good news! emLab qualifies as an educational organization through the GitHub Education program, and as a UCSB staff member you qualify for the individual educational discount. So, once you’ve signed up for a free account on GitHub… Step 2: Register as a researcher Go to the GitHub Education page and register as a researcher Note: this is why you should use your @ucsb.edu email for step 1. Click on the “Get benefits” link in the top right-hand corner and follow the directions to upgrade your account to a “Pro” account for free. You may need to take a picture of your UCSB ID card to submit as part of this process. GitHub may also periodically ask you to re-verify your eligability to qualify for this program. Step 3: Get invited to the emLab GitHub organization Send Erin O’Reilly a Slack message (or an email if you must… eoreilly@ucsb.edu) with your new GitHub username so you can be added to the emLab GitHub page! The emLab GitHub page is where the repositories for all emLab projects live (more on this later), and once you are a member of the organization you will be able to create new public and private repositories that appear here (as well as on your personal page). Step 4: Install Git If you’re very very lucky, Git will already be installed on your computer. Open the shell for your opperating system. If you’re using Mac OS X, this is called Terminal. If you’re using Windows, you have multiple types of shells, but you should be using a Git Bash shell (NOT Power Shell). The easiest way to find out whether Git is already installed on your machine is to type the following: git --version ## git version 2.20.1 (Apple Git-117) If it returns a version number, you already have Git installed! However, if it returns something like git: command not found, you need to install Git. There are a number of different ways to install Git. Stand-alone installers exist for Mac OS X and Windows. If you’re using Linux, you probably already know how to install Git. If you’re using Mac OS X, Git can also be installed as part of the XCode Command Line tools, or you can also install it using Homebrew. If you’re interested in either of those options, follow the cooresponding directions in Jenny Bryan’s tutorial. If that sentence doesn’t mean anything to you, download the installer from the link above and follow the prompts. Once you’ve installed Git via whichever method you’ve chosen for your operating system, open the shell again and retype the same command to verify that the installation was successful: git --version ## git version 2.20.1 (Apple Git-117) It should now return a version number. Step 5: Tell Git who you are Git needs to know a little bit more about you in order to play nicely. In particular there are two things that it’s helpful to configure: 1) The name that will be associated with any commits you make, and 2) the email address asssociated with your GitHub account. To set these two things, type the following into the shell using your name and email: git config --global user.name 'Jane Doe' git config --global user.email 'jane@example.com' The user name input here should be your full name (i.e. it does not need to be the same as your username for GitHub), but the email DOES need to be the same as that associated with your GitHub account. You can then check to make sure these were entered correctly by typing: git config --global --list Step 6 (optional): Store your credentials (so you don’t have to type your password every time) Git will sometimes want to make sure you are you when performing certain operations. For example, when cloning a private repo or when you want to push changes to a repo. If you don’t want to do this every time, you can tell Git to remember your password too. You can read more about Git’s credential management here. On your terminal, navigate to a repository on your computer. (You can also use the Terminal pane within RStudio) and type the following into the shell: # Tell git to use the credential.helper git config --global credential.helper store # git pull (or git push) will prompt you to enter your password git pull What we just did was to tell Git to store our credentials. So, after typing them this one time, you should not need to type it again. Step 7 (optional): Install a client for Git to make your life easier If you actually tried step 6 and you’re still reading this, you probably don’t usually spend a lot of time running commands in the shell and the last step didn’t make a lot of sense. If that’s the case, you might want to also install a Git client in order to help you visualize what Git is actually doing. You do not need a Git client to take advantage of version-control functionality of Git, as everything can be done using the shell (as in the previous step). However, the shell is not user-friendly. There are a number of Git/GitHub clients that you can download to interact with Git and GitHub in a more visual way. If you use RStudio, there is a very basic Git client built in that may be enough to get you started (more on this later). Other nice free Git clients include: GitKraken (available for all platforms, plus the logo octopus is pretty sweet…) GitFiend (cross-platform) SourceTree (has some problems on Mac OS X) GitHub Desktop (not available for Linux) GitUp (only for Mac OS X) There are many more. See Jenny Bryan’s tutorial if you’re not satisfied with those choices. Once you’ve installed a Git client, follow the directions to connect to your GitHub account. Once you’ve done this, try opening the local version of the repository you made in step 6, and notice the nice visual representation of the changes you made. 8.7.4 General guidelines for using GitHub at emLab In general, each emLab project should have its own repository. There may be some cases in which multiple repositories may be associated with the same project, but this should be avoided if possible. The project repository should be created within the emLab GitHub page (exceptions may exist for example if a partner organization requires that the project repository be created within their organization’s GitHub page). Repositories can be made public or private when they are created (depending on the nature of the project) while the project is ongoing, but should be made public when the project is complete. Since many previous (and ongoing) projects were created within the personal GitHub pages of emLab members, the ownership of these repositories should be transferred to the emLab GitHub page at the conclusion of the project if possible. In order to ensure that the relevant researchers are notified of issues and other activities, researchers should “watch” or “subscribe” to repositories in which they work. 8.8 Zotero emLab uses Zotero to collaboratively collect, organize, and cite publications. We organize publications into Group Libraries which can be at the project or paper level. Our account – emlab-ucsb – has unlimited storage and there is no limit to the number of people you can add to a library. In Zotero, storage for a library only counts against the owner, so the emLab account must be the owner of the library for access to unlimited storage. 8.8.1 Making emLab the owner of a library If creating a new group library, slack/email Erin (eoreilly@ucsb.edu) and she can directly create the library under the emLab account. If you are the owner of an existing library and would like to transfer ownership to emLab, first invite emlab-ucsb to be a member of the library. Once that invitation has been accepted, then go to “Group Settings” for the library and in the bottom right of the page, select transfer ownership to the emLab account. 8.8.2 Saving publications to a library To use Zotero properly, you need to install the Zotero Connector for your browser in addition to the Zotero desktop app (see this page for downloads). The most convenient way to save publications to Zotero is through Zotero Connector. The Zotero Connector allows you to add publications from your browser to Zotero with a single click. The “save” button shows up in the upper right corner of your browser and the symbol appears differently depending on the type of reference you are viewing (e.g. book, PDF, webpage). After you click the save button, a popup will appear that allows you to select the library to save the reference to. Read more about saving items to Zotero here. 8.8.3 Zotero integration with GoogleDocs and Word Zotero is a great resource for adding references to a manuscript. It is integrated into both Word and GoogleDocs for easy use. As a note, you have to take extra steps to ensure that your references remain linked when switching between Word and GoogleDocs. See this document for more information about moving documents with Zotero citations between word processors. 8.8.3.1 Adding a citation to your document In both Word and GoogleDocs, Zotero shows up as a separate tab/menu item for you to choose from. For example, this is the Zotero tab in Word. To add an in-text citation, place your cursor after the statement you want to reference and then click on “Add/Edit Citation.” This brings up a Zotero search bar that allows you to search for a reference within your libraries based on a keyword or author. As you type, Zotero brings up options that you can select from. Once you select the citation, either insert a comma to add another citation or select enter to add the reference. Note: If you are adding a citation for the first time to a document, you will be asked to select the citation style. This allows you to add a reference style based on your target journal. 8.8.3.2 Adding a bibliography to your document The most amazing thing about Zotero is that it automatically generates a bibliography for you based on your in-text citations. To add a bibliography, simply place your cursor where you want to add your reference list and select “Add/Edit Bibliography.” It will add all of the references for you based on the citation style selected. 8.9 Project management platforms There are many available cloud-based project management tools and platforms to help facilitate project management and track milestones and deliverables. It is up to each project manager and team to select a system that works best for their individual project and the team. See project execution section for more details and emLab templates for work planning. 8.10 Data and code standard operating procedure Since we love GitHub and open data science, we have a whole Bookdown dedicated to data and code standard operating procedures for emLab. In this document, you will find information about data storage, metadata, tidy data, code style guides, code reproducibility, high performance computing, and more. This is a living document, so please feel free to suggest updates in the data-streamlining slack channel. "], ["project-management.html", "Section 9 Project management 9.1 Setting a project up for success 9.2 Project execution 9.3 Project communications 9.4 Wrapping up a project", " Section 9 Project management 9.1 Setting a project up for success Yay we have a new emLab project! But now what? To set a solid foundation for a project, the following meetings and activities are required. 9.1.1 Kickoff meetings Operations team handoff meeting Before a project kicks off, Michaela and/or Amanda will meet with the project manager to give them an overview of how this project was conceptualized, what deliverables are included in the scope of work, how flexible or rigid the timeline and deliverables are, the envisioned project team composition or plans for recruiting and hiring, and any other relevant details about the funder, project team, partner, or body of work. This will help ensure a smooth handoff between project scoping and project execution. Planning and strategy meeting between the project manager and project PI(s) Project managers serve as an extension of the PIs and work with them to keep projects on track. Since each project has unique project management needs, this meeting will be used to build repertoire between the project manager and PI(s) and to set clear expectations. The following are potential discussion topics: Review objectives and scope of the project (i.e., get the PM up to speed on what the project is all about) Discuss project team composition and any new hires/internal capacity needs Identify undergraduate or graduate student needs Define the roles and responsibilities for each project member (if possible at this time). Questions to consider: What would the PIs like the project manager to be responsible for? If multiple PIs, what is each PI responsible for? What are the other team members responsible for? Are there preferences or need-to-knows about scheduling or internal communication? Discuss project partners/collaborators. Who is responsible for external communications with partners? Are there any concerns about the project that need to be discussed? Identify next steps for project launch meetings Internal project kickoff meeting The main objective of this meeting is to align project team members on the scope of work and project objectives, discuss the project approach, identify roles and responsibilities, and discuss project organization and communications. This meeting will be attended by the full project team. The objectives of this meeting are to: Align the team around the SOW (timeline, deliverables, approach) Identify high-level goals, uncertainties, and potential challenges Get a sense of the related work to date and available data Align on project/team logistics (capacity, meeting frequency) and immediate next steps Here is a draft agenda: Quick introductions if needed (i.e. if there are new team members) Review the project objectives, deliverables, and timeline as outlined in the scope of work Review team structure and outline responsibilities (if possible/needed at this time) Project organization and communication strategy Review the project name for the project to use across platforms (all lowercase with dashes to separate words) Review how the team is going to organize work across platforms Decide the internal team meeting cadence Discuss the meeting cadence with partners or external collaborators Discuss and refine approach as outlined in the SOW Identify high-level goals, uncertainties, and potential challenges How well defined vs. flexible are the approach and deliverables? Do we have a good sense of the data requirements? What other projects or work does this project leverage? Identify next steps for the project External project launch meeting Once the project team has met, the project manager should schedule a kickoff with the project partner (if applicable). The discussion topics will vary based on the level of engagement the partner would like, but potential items to discuss are: Project and people introductions: review and discuss project objectives and approach, and introduce the project team. In this, also tell the partner who their emLab point of contact will be. Meeting and reporting: discuss the meeting and reporting frequency if not already determined. Pivot points: reiterate that in any research project things can change. Discuss approach for making joint decisions about taking different approaches, modifying project scope, and communicating/documenting changes as the project evolves. 9.1.2 Setting up your project on the emLab platforms See Chapter 8 for a more detailed explanation of emLab’s platforms. Once your team has decided on a project name (note: must be all lowercase with dashes to separate words), set up project specific folders/channels on the following platforms: For Google Calendar: remind everyone to keep their calendar up to date for scheduling purposes. Request access to detailed PI calendars if needed. For Slack: to create a channel, click on the plus symbol next to channels and fill out the channel information (Name, Purpose, and Send invites to). If you need to invite guests to the channel, please reach out to Erin (eoreilly@ucsb.edu). For Zotero: send Erin (eoreilly@ucsb.edu) the name of your folder and the Zotero usernames for all of the team members who need access. For Shared Drive: create a new project folder in the emlab/projects/current-projects folder. Each project folder must contain the following 6 folders: data: this data folder will contain a data_overview spreadsheet and all of the intermediate datasets as well as output datasets associated with the project (see emLab’s data and code standard operating procedure for more on this). Be sure to also add a copy of your final datasets to the emlab/data folder and data directory. deliverables: final reports, paper manuscripts, other final deliverables not related to data outputs grant-reporting: grant reports for funders meetings-and-events: meeting notes, agendas, documentation for workshop/event planning presentations: any presentations created for the project project-materials: everything else that does not fit into one of these folders (i.e. drafts of methods, literature review, working documents/slides, etc.). It’s often a good idea to create an admin subfolder to house the SOW for easy referencing. From here, each project can add sub-folders as they see fit within these 6 folders. For GitHub: The structure of each emLab repository on GitHub will likely vary depending on the needs of the project, but the following structure is suggested as a starting point. Project managers can have a researcher set up the repo for the team. A documents (or docs) folder may be useful for storing code files that are used to generate text-based documents or presentations. Types of files that might live here include things like markdown files. A results folder may be useful for storing plots or other types of results generated by the project. Some discretion needs to be used here, as some results may actually be considered to be “processed” or “output” data. However, results in the form of figures or workspace image files might live here. A scripts folder may be useful for storing the code files that do everything from processing the raw data to running the analysis and generating outputs. A functions folder may be useful for storing the code files in which functions that are used by many scripts may be stored. Different types of projects may require more or fewer folders and these are only meant to act as suggestions. Regardless, the structure of the repository should be sufficiently organized such that it can be easily navigated and understood by others by the time the project is completed. Note on a repo inside a repo: sometimes a project may have more than one paper or analysis sections. In some scenarios, we might want to have multiple “paper folders” within a “project folder.” This would imply that we will have a repo inside a repo. If that is something that makes sense for you, your project, and your team, then git submodules are your solution. If you want to read more on when / how to use submodules, visit the documentation page here. Including submodules in your workflow is simple. Here’s an example: you are working on a big project called “Blue Future.” The project has six PIs, 13 Research Specialists, two PostDocs, and three PhD Students. After a long kick-off meeting, the team realizes that the project will produce two papers and a ShinyApp. You are all determined to keep everything in the same folder, but correctly categorized and organized. As such, you go to GitHub and create the following four repositories: blue-future paper1 paper2 shiny-app You’ll clone the blue-future repo into your computer, using the usual: git clone https://github.com/emlab-ucsb/blue-future.git Now, instead of cloning the repos for each paper and the app into their own folder, you’ll navigate into your local blue-future folder. Then, instead of cloning them there, you can just do: git submodule add https://github.com/emlab-ucsb/paper1.git This will clone the paper1 repo, but not without first telling the blue-future repo about it (just so that you don’t end up tracking things twice). You can repeat the operation for paper2 and shiny-app. That’s it! 9.2 Project execution 9.2.1 Moving from SOW to a work plan The overall goal of a work plan is to define and track the activities needed to achieve project deliverables. They are a way to map out deadlines, who is responsible for completing a task, and how certain outputs may be leveraged for a publication. The scope of work serves as the basis for developing a work plan but note that the level of detail included in a scope of work varies from project to project. Sometimes work plans write themselves and other times the project phases and activities are less clear The project manager and PI planning meeting should provide initial thoughts and clarifications on the scope of work, and afterwards the project manager should be able to build out a skeleton work plan for the project. Every step of the project does not need to be planned immediately, but a general sense of the project phases is useful. Oftentimes projects undergo an exploratory phase that is composed of brainstorming meetings, literature reviews, research question refining, and initial method testing until a final approach is determined and the work plan will continue to evolve through these meetings. We recognize that each team member has a different method for keeping track of tasks. It is up to the project manager to figure out what system and level of detail works best for them and their team. We have put together a work plan template here that can be copied and adapted to your project’s needs. A special note on projects that contain both academic publications and ‘applied’ research products as deliverables (or if the team is interested in writing a publication outside of the responsibilities for the project). When developing the work plan, try to map out the common activities and interim outputs that can inform both applied products and academic publications to help increase efficiencies and ensure that the paper deliverable doesn’t feel tacked on at the end. As you progress through a project, capture methods, results, figures, and discussion topics throughout to aid your future selves in writing a paper. An example of this can be seen in the “example” tab of the work plan template. 9.2.2 Adaptive management Research is not a linear process. There are often many avenues we explore before deciding how to best move a project forward. So just a reminder to be kind to ourselves if we are struggling to figure out how to move forward or feel like we are spinning our wheels. Credit: Allison Horst To support this type of work, we often employ adaptive management strategies. Core to these strategies are: Clear and proactive communication about timelines, feedback needed, unanticipated challenges, pivot points, new responsibilities, capacity limitations due to other project deadlines, etc. Understanding the sequential and/or interdependent nature of work. For example, if one piece is delayed or pan out as expected, how will that impact other parts of the project? Flexibility and ability to integrate new solutions into workflow. Sometimes partner priorities change, data is not available, or another challenge or opportunity arises that require you to pivot the project in a new direction. Pivot points are a signal that something in the project has changed, they are not a sign of failure. When a pivot point occurs in a project, first have a frank conversation with the project team (i.e. why is a certain approach not working? What topical avenues are we interested in exploring? How can we better service our partners?). Then communicate with the project partner about the evolution of the project and why something may not be working, potential new directions, and any adjustments to project timelines and deliverables. Be sure to document any significant pivot points in writing. 9.2.3 Running efficient meetings Since everyone’s time is valuable, we want to try to avoid the stigma that meetings are time sucks by running efficient meetings. These articles – How to run effective meetings and A Mantra for Facilitating Team Science Virtually to Get the Job Done – provide a good overview of tactics for facilitating efficient meetings. Before scheduling a meeting, run through these questions to determine if a meeting is necessary: Preparing for the meeting Planning and preparation are key to running efficient and effective meetings. Before a meeting is scheduled ask yourself the following questions: Why are we meeting? What do we need to walk away with? How will we get there? Who needs to be a part of the meeting? Use these questions to draft a meeting agenda and inform the participant list. The agenda does not need to be long, but at a minimum should include: Meeting objectives (e.g., brainstorming, decision-making, updates, etc.) Agenda topics/key discussion points In drafting a meeting agenda, think about the utility or necessity of prep work. Is someone presenting? Do people need to review a document in advance? Do people need to be prepared to lead a part of the discussion? Who is facilitating the meeting? If that is not you, make sure to prep the facilitator with all the appropriate information. Be sure to give attendees an appropriate amount of time to prep so the meeting runs smoothly. Even if no prep work is needed, try to circulate an agenda at least 24 hours before the meeting. As we work with partners around the world, facilitating effective virtual collaborations is important to project success. Expert facilitator and NCEAS senior fellow, Carrie Kappel promotes four principles to keep in mind as you design and prepare your meeting: interactivity, accessibility, connectivity, and efficiency. Thoughtful meeting preparation, clear articulation of meeting objectives and goals, delegating responsibilities, and active facilitation are all important to successful meetings. During the meeting Every meeting will differ depending on the goals and objectives and participants, but ultimately you want to connect and engage participants to achieve the meeting objectives as efficiently as possible. Kickoff the meeting with a review of the meeting objectives so everyone understands why they are meeting and what collectively they are aiming to achieve by the end of the meeting. Invite clarifying questions, delegate any responsibilities you need to that you haven’t already (e.g. note taking), and jump into the agenda. Here are some tips on facilitation that draw on Atlassian’s blog if you want to read more and emLab’s collective experience: Embrace and own your role as facilitator - which is namely to manage time, encourage participation, and ask questions. Try to avoid wearing the meeting participant hat as well. Create an interactive agenda where different people lead different agenda items or use interactive tools, such as jamboard for brainstorming sessions If the conversation is going too into the weeds, come back to the meeting objectives/purpose (one reason why it’s great to state this at the beginning of the meeting) “Check for understanding” - feel free to ask clarifying questions or ask someone to clarify their point if it’s unclear. Some other example questions for facilitating conversations include: Can you expand on that point? That last point is interesting, but seems counterintuitive - can you explain your intuition around that? Can you summarize that last point for me? What would that look like? What is the next step? Be mindful of power dynamics in a meeting and work to amplify quieter voices. Building in breakout groups, writing ideas on post-it notes or a jamboard, or allowing folks to follow-up with additional ideas after the meeting are helpful approaches to engaging all voices. The meeting agenda and subsequent notes should at minimum include the following information: Date Meeting objective(s) Attendees Key points or decisions Next steps, including action items and who is responsible for them Reserve the last 5-10 minutes of the meeting to recap the meeting and review the next step tasks. After the meeting Once the meeting is over, circulate the meeting notes document with attendees within 24 hours if possible. Highlight and bold next steps and action items at the top of the document. Sometimes a quick summary of key decisions and next steps in Slack is also helpful. 9.2.4 Partner engagement A key tenant of emLab projects is working with partners to solve real world problems. It is the responsibility of the project manager, in coordination with the project team and PIs, to make sure that the project outputs, outcomes, and deliverables meet the expectations of our partners. Clear and open communication on project status, challenges, and milestones are important to managing expectations. If any critical aspects of the project have changed or need to change, first discuss with the PI(s), then align on a strategy for communicating this with the partner. 9.2.5 Author contributions Since most of our projects include a publication aspect, it is best to communicate about author expectations and contributions as early as possible. Determining authorship is ultimately the responsibility of the project leads (i.e. principal investigator and/or first author), but because author contribution is not always straightforward, we follow McNutt et al. 2018 and others in recommending the Contributor Roles Taxonomy (CRediT) system. For a simplified version of this most relevant to our project infrastructure, feel free to use and modify our Author Contribution Template, which allows individuals to identify their contributions or to opt-out of participation in a paper. We recommend discussing authorship expectations early in a project to avoid future complications. 9.3 Project communications It is the responsibility of the project manager to work with the project team (and partners, if applicable) to determine the project’s external communication and outreach needs. In general, we want to highlight project successes, key results, how our results were used, and project outputs (publication/report, tool, media coverage, talks, etc.). To support these project highlights, the project manager should work with the communications team on the following: Drafting content for the project’s page on the website within the first month of kicking off a project Note: please ping Erin if a new member joins the team so she can update the project page Keeping the communications team informed of publications, seminars/webinars, or press coverage and working with them to highlight successes. Advanced notice is much appreciated. When reaching out to the comms team, please send a short summary (bullets work) of what you want to highlight, any partners we should work with/tag, and overarching relevance of this work. The comms team will draft visuals and text for the project manager to review for clarity and framing. When a project ends, sending the communications team a summary of key findings and outcomes to add to the project page 9.4 Wrapping up a project When a project is completed, make sure that all project files are in Shared Drive, add data to the data-directory as appropriate, and move the project folder to emlab/projects/archived-projects. Finally, schedule a project exit interview with the full project team and emLab’s Executive Director. The purpose of this meeting is to capture lessons learned, evaluate success, and identify potential next steps. The ED will run this meeting so all project team members can fully participate. Below is a draft agenda for the exit interview: What aspects of the project went well? What were our greatest successes in terms of scoping, deliverables, team structure, partners, etc.? What were the challenges? What could we have done differently to improve the project process or outcomes? Did the client receive what they expected, and on time? Lessons learned: reflect on the successes and challenges to identify concrete strategies for future projects Identify potential next steps (if applicable) Did the project uncover new and interesting research questions through the project? Would the existing sponsor be interested in this follow-up work or are there other partners who would be interested? If yes, develop a scope of work for this new body of work That’s it! Take a moment to congratulate yourself and the team for completing the project! "], ["communications-and-outreach.html", "Section 10 Communications and outreach", " Section 10 Communications and outreach As a team committed to conducting research for real-world impact, science communication plays a large role in the dissemination of our work. To showcase emLab’s impact, we employ a variety of platforms and tactics. emLab’s main communication channels include: - Our website: houses information about programs, projects, data and tools, publications, media coverage, our blog, and about our team - Monthly newsletter: highlights team announcements, new work, and spotlights of new and completed projects - Social media – Twitter, Instagram, LinkedIn – shares information about project success stories, new publications, team profiles, and more Our communications team works in coordination with project managers and University staff to produce outreach strategies and materials. If you have any communications questions or requests, reach out to Erin (eoreilly@ucsb.edu). "], ["onboarding.html", "Section 11 Onboarding 11.1 Relocating to Santa Barbara 11.2 Employment paperwork 11.3 Employee accounts 11.4 University benefits 11.5 Relevant listservs and resources 11.6 Your first week at emLab 11.7 Santa Barbara recommendations", " Section 11 Onboarding Welcome! We are excited to have you join the emLab team. We hope that these onboarding resources, guidelines, and tips will make your transition to emLab seamless and enjoyable. To give you the lay of the land, emLab is part of UC Santa Barbara (UCSB) and is housed within two main departments: the Marine Science Institute (MSI) and Bren School for Environmental Science & Management. Our offices span MSI and Bren, and the majority of our grants and purchases are run through MSI. This section provides onboarding information at both the University and emLab level. 11.1 Relocating to Santa Barbara Santa Barbara is a vibrant historical city, teeming with arts and cultural experiences, culinary adventures, stunning landscapes, beautiful parks, and outdoor activities. Check out this Unofficial Guide to Housing to learn more about the neighborhoods in Santa Barbara. As a note, Santa Barbara does have high housing costs and demand in comparison to most of the United States, and can be a challenging destination to relocate to. You may find the following resources helpful, but we also encourage you to reach out to our Operations Manager (eoreilly@ucsb.edu) if you need additional insight on short- or long-term housing. Sign up to receive housing alerts from the Bren Random listserv UCSB Off-Campus Housing Office Santa Barbara Craigslist Many local real estate search engines also include professionally managed rentals in their results Note that you may be more competitive as a rental applicant if you are prepared to provide a detailed, current credit report; letters of rental reference; evidence of income (emLab can provide an employment offer letter); and a completed standard rental application form when viewing a property or contacting potential landlords. 11.2 Employment paperwork Once you have accepted an offer of employment with emLab, you will be contacted by Lyndi Swanson in the Personnel Unit of the Marine Science Institute to schedule a New Hire appointment. If possible, please schedule your appointment with Lyndi prior to your first day of work, as this will ensure that other services provided through the University will be ready when you arrive. Lyndi will walk you through all of the University-required employee paperwork during your appointment. She will send you an email with information and further details on the paperwork you need to fill out. The employee paperwork you will need to fill out includes: Employment data form I-9 verification State Oath of Allegiance Patent Acknowledgement W-4 Direct deposit form (if desired) After your appointment, look for an email from Lyndi with your Employee ID number. This Employee ID number is necessary for setting up all other University accounts. 11.3 Employee accounts Once you have your employee ID number, you will be able to set up your UCSBnetID, which will give you access to computing services and other campus resources for staff and researchers. Creating your UCSBnetID will generate your UCSB email (netid@ucsb.edu) and will give you log-in access to all UCSB platforms. Here’s a brief overview of the different UCSB accounts and websites: Employee ID Number: payroll number assigned to you; used to create UCSBnetID and email UCSBnetID: used to log into all UCSB accounts (UCPath, Kronos, etc.) Bren Account: used to connect to Bren wifi and log into Bren windows computers UCPath: site that contains information on paychecks and benefits Kronos: timekeeping system to input sick/vacation hours There are a couple of optional services you can set-up with your UCSBnetID: Join the Transportation Alternatives Program (TAP), offering discounted bus passes ($31/month), a limited number of free on-campus parking hours, and other benefits for choosing low carbon transit. Visit Parking Services on campus to sign up for campus staff parking if you do not wish to join TAP (for a monthly payroll deduction of $37.50). Receive discounted membership at the UCSB Recreation Center. Obtain a campus ID card for verification of employment and access to the library, buildings after hours, and gym. This is not required to get into any of our offices during normal work hours. There is a one-time $30 fee per card that employees must pay themselves. 11.4 University benefits UCSB hosts a New Employee Orientation for all new employees campus-wide. They provide an overview of the University and review the different benefit options available to you. If you are unable to attend the New Employee Orientation, you can also explore your benefits on your own through the New Employee Orientation slideshow and checklist. You have 31 days from your start date to select your health benefits (i.e. medical, dental, and vision plans) and 90 days from your start date to choose your retirement benefits. This roadmap can help guide you through the benefits selection process. Here are some additional resources to help support the selection of your benefits: Review the Your Benefits at a Glance overview document For healthcare, explore the Complete Guide to UC Health and Welfare Benefits For retirement, delve into the Retirement Benefits Decision Guide 11.5 Relevant listservs and resources This section outlines points of contact and resources for more general support. For Bren Hall building and shower keys, and to make copies/scan/fax, contact Sara Mata (sarajoymata@ucsb.edu, 2400 Bren Hall). For IT support: reach out to the IT department for the building you are housed in – Bren (compute@bren.ucsb.edu) or MSI (help@msi.ucsb.edu). For operations support, read the team guidelines and talk to operations team about: Facilities issues (like hanging a whiteboard, getting a bookcase, fixing a heater) Travel planning, allowable expenses, visa applications, and reimbursements Reserving a meeting room and/or planning an event involving food Ordering office supplies, computer equipment, or field gear For information on Bren and MSI news and events, sign up to receive updates from the following listservs: Bren-Alerts Bren Researchers - email Corina Aguiar to be added (corina@bren.ucsb.edu) Bren Random MSI News 11.6 Your first week at emLab Your first week at emLab will mainly focus on setting up your UCSB accounts, introducing you to emLab and how we work, and getting you settled in your new role. Starting with the basics, we will give you a tour of your office and the building it is situated in, and get you set up with an office key and wifi. Depending on availability, we will either provide a computer to you or order a new one with the necessary specs. Key acquisition methods depend on which building your office is located in. Erin will initiate the first email with the correct contact and, for reference, Kim Taylor (kim.taylor@ucsb.edu) handles keys for MSI and Sara Mata (sarajoymata@ucsb.edu) handles keys for Bren. If starting on a Monday, you will also be able to meet the team at our Monday Morning Meeting. Here’s a list of the emLab team. There are four key meetings that will occur during your first week: Meeting with Michaela, emLab’s Executive Director: an introduction to emLab and our work culture and values Meeting with Erin, emLab’s Projects and Operations Manager: an overview of emLab’s platforms, resources, and workflow Meeting with your supervisor: a deeper dive into your job duties and the project team you will be working with. You will also review the cadence of check-in meetings. And last but not least, a welcome lunch or happy hour! Once you have your UCSB email, Erin will add you to all of the relevant emLab platforms (e.g., slack, shared drive, etc.). If you have any questions as you start getting up to speed, please don’t hesitate to reach out to Erin or your supervisor! 11.7 Santa Barbara recommendations If you are new to the area (or just looking for new recommendations), here’s a list of good food, drinks, and activities in Santa Barbara. Let Erin know if there are other recs you want to add to this list! Drinks Beer M Special Captain Fattys Institution Ale Third Window (they also have amazing smash burgers on the weekend) Lama Dog/Topa Topa Figueroa Mountain Biergarten Wine Deep Sea (best view ever!) The Valley Project Municipal Winemakers Pali Margerum Cocktails Good Lion Imperial Shaker Mill Coffee Dune Handlebar Caje (the Arlington one is awesome) Dart Food Breakfast Dawn Patrol Scarlett Begonia Hook and Press (donuts) Daily Grind (smoothies, scones, muffins, breakfast burritos) The Shop Lunch/dinner Mony’s (mexican) Lily’s Tacos (mexican) Altamarinos (mexican) Los Agaves (mexican) Apna (indian) Empty Bowl (thai) Sama Sama (southeast asian) The Lark (farm to table) Loquita (tapas, gin and tonics) Bettina (pizza) Secret Bao (asian with some fun fusion dishes like udon carbonara) South Coast Deli (sandwiches and salads) Blue Owl Yellow Belly Other Rory’s (ice cream) McConnells (ice cream) Oat Bakery (bread) Hikes Inspiration point Cathedral peak 3 pools 7 falls Gaviota peak Romero Rattlesnake Dives Shore: Refugio Boat: any of the Channel Islands Places and activities Cold Springs Tavern (beer, tri-tip and music on the weekend) Red Rock (swimming and jumping off rocks in the river) Knapps Castle More Mesa Beach Wine tasting in the Santa Ynez valley Ellwood Bluffs Beer/wine tasting in the funk zone East Beach and Leadbetter are the easiest to post up at for a beach day Other things Farmer’s market Downtown: Tuesday afternoon and Saturday mornings Goleta: Sunday CSA boxes (e.g. farmcart organics) "],