From 9f2d7b1ee43847269e7e59b35bf9f3adec00f930 Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Thu, 27 Jun 2024 14:30:17 +0100 Subject: [PATCH 01/16] Movement: Updated all hyperlinks --- docs/Projects/DevoWorm.md | 4 ++-- docs/Projects/worm-movement.md | 30 +++++++++++++++--------------- 2 files changed, 17 insertions(+), 17 deletions(-) diff --git a/docs/Projects/DevoWorm.md b/docs/Projects/DevoWorm.md index 831229a7..71fef69c 100644 --- a/docs/Projects/DevoWorm.md +++ b/docs/Projects/DevoWorm.md @@ -6,13 +6,13 @@ educational, academic, media-related and collaborative opportunities associated ## Roadmap -DevoWorm is currently divided into three loosely-knit interest areas: developmental dynamics, cybernetics and digital morphogenesis, and reproduction and developmental plasticity. While our main interest is in the nematode *Caenorhabditis elegans*, we are also interested in cross-species comparative work. +DevoWorm is currently divided into three loosely-knit interest areas: developmental dynamics, cybernetics and digital morphogenesis, and reproduction and developmental plasticity. While our main interest is in the nematode _Caenorhabditis elegans_, we are also interested in cross-species comparative work. **Developmental Dynamics** currently involves using secondary data collected from embryos along with bioinformatic and data science techniques to answer questions regarding the process of early embryogenesis and the timing of later morphogenesis. To address these problems, we have used number of innovative approaches. **Cybernetics and Digital Morphogenesis** has involved using platforms such as Morphozoic (Cellular Automata) or CompuCell3D (Cellular Potts Model) to better understand physical interactions during embryogenesis and morphogenesis. We have also explored the use of cybernetic models and concepts to better understand the general process of embryogenesis. -**Reproduction and Developmental Plasticity** involves utilizing an evo-devo approach to understand *Caenorhabditis elegans* more generally. Our existing datasets and papers include a focus on larval development and life-history processes. This area of the project also features primary empirical data, based on formal experimental design. +**Reproduction and Developmental Plasticity** involves utilizing an evo-devo approach to understand _Caenorhabditis elegans_ more generally. Our existing datasets and papers include a focus on larval development and life-history processes. This area of the project also features primary empirical data, based on formal experimental design. Objective | Examples --- | --- diff --git a/docs/Projects/worm-movement.md b/docs/Projects/worm-movement.md index c2190729..eb101464 100644 --- a/docs/Projects/worm-movement.md +++ b/docs/Projects/worm-movement.md @@ -17,7 +17,7 @@ For more information, please visit the above pages. Current roadmap --------------- -###[STORY: Build a test suite for the simulation from WormBehavior database](https://github.com/openworm/OpenWorm/issues?milestone=19&state=open) +###[STORY: Build a test suite for the simulation from WormBehavior database](https://github.com/openworm/OpenWorm/issues?milestone=19&state=closed) As a scientist or developer, I want to be able to run a test suite against the simulation that will show me how close the model is to real data. @@ -25,7 +25,7 @@ In order for a model to demonstrate scientific value, it has to make falsifiable This story breaks down the epic to predict behavior from the WormBehavior database. -###[EPIC: Correctly predict 80% of wild type (N2) behavior in WormBehavior database](https://github.com/openworm/OpenWorm/issues?milestone=22&state=open) +###[EPIC: Correctly predict 80% of wild type (N2) behavior in WormBehavior database](https://github.com/openworm/OpenWorm/milestone/22) This epic is to have a simulation that can demonstrate it can predict (and therefore reproduce) 80% of the data collected about the N2 worm in the WormBehavior database. This means building a training set and a test set that are kept separate from each other, using the training set to tune up the model, then generating predictions, and comparing them against the test set, and doing some cross-validation). @@ -43,28 +43,28 @@ Associated Repositories **OpenWorm Port of Schafer Lab's Worm Analysis Toolbox 1.3.4** -- https://github.com/openworm/SegWorm (original MATLAB code, static) -- https://github.com/JimHokanson/SegwormMatlabClasses (Jim's MATLAB fork, now static) -- https://github.com/openworm/open-worm-analysis-toolbox (active Python port; formerly movement_validation) +- [https://github.com/openworm/SegWorm](https://github.com/openworm/SegWorm) (original MATLAB code, static) +- [https://github.com/JimHokanson/SegwormMatlabClasses](https://github.com/JimHokanson/SegwormMatlabClasses) (Jim's MATLAB fork, now static) +- [https://github.com/openworm/open-worm-analysis-toolbox](https://github.com/openworm/open-worm-analysis-toolbox) (active Python port; formerly movement_validation) **Cloud Computing** -- https://github.com/openworm/movement_validation_cloud, forked from -- https://github.com/joebowen/movement_validation_cloud +- [https://github.com/openworm/movement_validation_cloud](https://github.com/openworm/movement_validation_cloud), forked from +- [https://github.com/joebowen/movement_validation_cloud](https://github.com/joebowen/movement_validation_cloud) **Worm Tracker File Format Specification and Parser** -- https://github.com/openworm/tracker-commons -- https://github.com/openworm/biological_data (placeholder repo to discuss worm video data) +- [https://github.com/openworm/tracker-commons](https://github.com/openworm/tracker-commons) +- [https://github.com/openworm/biological_data](https://github.com/openworm/biological_data) (placeholder repo to discuss worm video data) **André Brown's "Eigenworms" Code** -- https://github.com/aexbrown/Motif_Analysis (Deprecated in favour of Behavioural_Syntax below) -- https://github.com/aexbrown/Behavioural_Syntax (in MATLAB) -- https://github.com/AidanRocke/behavioral_syntax (Aidan Rocke's Python port) +- [https://github.com/aexbrown/Motif_Analysis](https://github.com/aexbrown/Motif_Analysis) (Deprecated in favour of Behavioural_Syntax below) +- [https://github.com/aexbrown/Behavioural_Syntax](https://github.com/aexbrown/Behavioural_Syntax) (in MATLAB) +- [https://github.com/AidanRocke/behavioral_syntax](https://github.com/AidanRocke/behavioral_syntax) (Aidan Rocke's Python port) **Brown Lab Multiworm Tracking Code** -- https://github.com/Behavioural-Genomics/tracking (not sure what this is, looks stale?) -- https://github.com/ver228/Multiworm_Tracking (Avelino's work) -- https://github.com/KezhiLi/Tracking_Hypo (Kezhi's work; the computer vision code) +- [https://github.com/Behavioural-Genomics/tracking](https://github.com/Behavioural-Genomics/tracking) (not sure what this is, looks stale?) +- [https://github.com/ver228/Multiworm_Tracking](https://github.com/ver228/Multiworm_Tracking) (Avelino's work) +- [https://github.com/KezhiLi/Tracking_Hypo](https://github.com/KezhiLi/Tracking_Hypo) (Kezhi's work; the computer vision code) From f5b226489510cb2d400d37725f4ee4eb5608baad Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Thu, 27 Jun 2024 14:40:47 +0100 Subject: [PATCH 02/16] Movement: including researcher's full names --- docs/Projects/worm-movement.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/Projects/worm-movement.md b/docs/Projects/worm-movement.md index eb101464..7fa83790 100644 --- a/docs/Projects/worm-movement.md +++ b/docs/Projects/worm-movement.md @@ -44,7 +44,7 @@ Associated Repositories **OpenWorm Port of Schafer Lab's Worm Analysis Toolbox 1.3.4** - [https://github.com/openworm/SegWorm](https://github.com/openworm/SegWorm) (original MATLAB code, static) -- [https://github.com/JimHokanson/SegwormMatlabClasses](https://github.com/JimHokanson/SegwormMatlabClasses) (Jim's MATLAB fork, now static) +- [https://github.com/JimHokanson/SegwormMatlabClasses](https://github.com/JimHokanson/SegwormMatlabClasses) (Jim Hokanson's MATLAB fork, now static) - [https://github.com/openworm/open-worm-analysis-toolbox](https://github.com/openworm/open-worm-analysis-toolbox) (active Python port; formerly movement_validation) **Cloud Computing** @@ -66,5 +66,5 @@ Associated Repositories **Brown Lab Multiworm Tracking Code** - [https://github.com/Behavioural-Genomics/tracking](https://github.com/Behavioural-Genomics/tracking) (not sure what this is, looks stale?) -- [https://github.com/ver228/Multiworm_Tracking](https://github.com/ver228/Multiworm_Tracking) (Avelino's work) -- [https://github.com/KezhiLi/Tracking_Hypo](https://github.com/KezhiLi/Tracking_Hypo) (Kezhi's work; the computer vision code) +- [https://github.com/ver228/Multiworm_Tracking](https://github.com/ver228/Multiworm_Tracking) (Avelino Javer's work) +- [https://github.com/KezhiLi/Tracking_Hypo](https://github.com/KezhiLi/Tracking_Hypo) (Kezhi Li's work; the computer vision code) From 16e750c65fd47da30aafd9fd79affb90864f51c2 Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Thu, 27 Jun 2024 15:00:04 +0100 Subject: [PATCH 03/16] Geppetto: updated urls --- docs/Projects/geppetto.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Projects/geppetto.md b/docs/Projects/geppetto.md index 55628da0..14379b60 100644 --- a/docs/Projects/geppetto.md +++ b/docs/Projects/geppetto.md @@ -5,7 +5,7 @@ In order to allow the world to play with the model easily, we are engineering [G Geppetto, is written in Java and leverages technologies like [OSGi](http://www.osgi.org/), [Spring Framework](http://www.springsource.org/spring-framework), [OpenCL](http://www.khronos.org/opencl/) and [Maven](http://maven.apache.org/). -Geppetto's frontend is written using [THREE.js](http://mrdoob.github.com/three.js/) and [WebGL](http://www.khronos.org/webgl/). Back-end / front-end communication happens via [JSON](http://www.json.org/) messages through [WebSocket](http://www.websocket.org/). +Geppetto's frontend is written using [THREE.js](https://github.com/mrdoob/three.js) and [WebGL](http://www.khronos.org/webgl/). Back-end / front-end communication happens via [JSON](http://www.json.org/) messages through [WebSocket](http://www.websocket.org/). The engine runs on on Eclipse Virgo WebServer deployed on an Amazon [Elastic Compute Cloud](http://aws.amazon.com/ec2/) Linux instance. From 172d4d6e6a79da90036b1111b9711faf32b0209c Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Thu, 27 Jun 2024 15:11:02 +0100 Subject: [PATCH 04/16] Optimization: updated language and urls --- docs/Projects/optimization.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/Projects/optimization.md b/docs/Projects/optimization.md index ca50c79e..132b457d 100644 --- a/docs/Projects/optimization.md +++ b/docs/Projects/optimization.md @@ -1,7 +1,7 @@ Optimization engine =================== -The Optimization engine uses optimization techniques like genetic algorithms to help fill gaps in our knowledge of the electrophysiology of *C. elegans* muscle cells and neurons. +The Optimization engine uses optimization techniques like genetic algorithms to help fill gaps in our knowledge of the electrophysiology of _C. elegans_ muscle cells and neurons. These two algorithms, Hodgkin-Huxley and SPH, require parameters to be set in order for them to function properly, and therefore create some "known unknowns" or "free parameters" we must define in order for the algorithm to function at all. For Hodgkin-Huxley we must define the ion channel species and set their conductance parameters. For SPH, we must define mass and the forces that one set of particles exert on another, which in turn means defining the mass of muscles and how much they pull. The conventional wisdom on modeling is to minimize the number of free parameters as much as possible, but we know there will be a vast parameter space associated with the model. @@ -15,15 +15,15 @@ Previous accomplishments Current roadmap --------------- -### [STORY: Muscle Cell model output closely matches that of real data](https://github.com/openworm/OpenWorm/issues?milestone=13&state=open) +### [STORY: Muscle Cell model output closely matches that of real data](https://github.com/openworm/OpenWorm/milestone/13?closed=1) -We will show that we have built a model of C. elegans muscle cell that matches data recorded from the nematode muscle cell. In part, we will use techniques of model optimization to fill in gaps in the model parameter space (deduce unmeasured parameters). The main technical challenge is tuning muscle cell passive properties and building a larger data set (more cell recordings). +We will show that we have built a model of _C. elegans_ muscle cell that matches data recorded from the nematode muscle cell. In part, we will use techniques of model optimization to fill in gaps in the model parameter space (deduce unmeasured parameters). The main technical challenge is tuning muscle cell passive properties and building a larger data set (more cell recordings). -### Bionet: training C. elegans with a specialized genetic algorithm +### Bionet: training _C. elegans_ with a specialized genetic algorithm -The C. elegans connectome is a neural network wiring diagram that specifies synaptic neurotransmitters and junction types. It does not however quantify synaptic connection strengths. It is believed that measuring these must be done in live specimens, requiring emerging or yet to be developed techniques. Without the connection strengths, it is not fully known how the nematode's nervous system produces sensory-motor behaviors. +The _C. elegans_ connectome is a neural network wiring diagram that specifies synaptic neurotransmitters and junction types. It does not however quantify synaptic connection strengths. It is believed that measuring these must be done in live specimens, requiring emerging or yet to be developed techniques. Without the connection strengths, it is not fully known how the nematode's nervous system produces sensory-motor behaviors. -Bionet is an attempt to compute the connection strengths that produce desired sensory-motor behaviors. This is done by a hybrid genetic algorithm that trains a large space of 3000+ weights representing synapse connection strengths to perform given sensory-motor sequences. The algorithm uses both global and local optimization techniques that take advantage of the topology of the connectome. An artificial worm embodying the connectome and trained to perform sensory-motor behaviors taken from measurements of the actual C. elegans would then behave realistically in an artificial environment. This is an important step toward creating a fully functional artificial worm. Indeed, knowing the artificial weights might cast light on the actual ones. +Bionet is an attempt to compute the connection strengths that produce desired sensory-motor behaviors. This is done by a hybrid genetic algorithm that trains a large space of 3000+ weights representing synapse connection strengths to perform given sensory-motor sequences. The algorithm uses both global and local optimization techniques that take advantage of the topology of the connectome. An artificial worm embodying the connectome and trained to perform sensory-motor behaviors taken from measurements of the actual _C. elegans_ would then behave realistically in an artificial environment. This is an important step toward creating a fully functional artificial worm. Indeed, knowing the artificial weights might cast light on the actual ones. Using the NEURON simulation tool as a fitness evaluation function, the pharyngeal neuron assembly has been trained to produce given activation patterns, reducing activation differences from more than 50% to less than 5%. Looking ahead, training worm locomotion behaviors using Movement Validation measurements as models will allow the neural network to drive the Sibernetic body model realistically. @@ -51,14 +51,14 @@ Associated Repositories HeuristicWorm - +Executes a genetic algorithm to train a model of a neuron

C++

bionet -Artificial neural network for training C. elegans behaviors +Artificial neural network for training C. elegans behaviors

C++

From 92badf0dbd55a9f412fcf8d3ed109778bfc165be Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Thu, 27 Jun 2024 17:52:13 +0100 Subject: [PATCH 05/16] Datarep: updated language and urls --- docs/Projects/datarep.md | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/docs/Projects/datarep.md b/docs/Projects/datarep.md index 2c262bff..c0a388f8 100644 --- a/docs/Projects/datarep.md +++ b/docs/Projects/datarep.md @@ -11,10 +11,10 @@ Using these different representations separately leads to ad hoc scripting for f Here is a list of some of the data sets that we have used so far: -- [The Virtual Worm (3D atlas of C. elegans anatomy)](http://caltech.wormbase.org/virtualworm/) -- [The c. elegans connectome (wiring diagram of neurons)](http://www.wormatlas.org/neuronalwiring.html) -- [Cell list of c. elegans](https://docs.google.com/spreadsheet/pub?key=0Avt3mQaA-HaMdGFnQldkWm9oUmQ3YjZ1LXJ4OHFnR0E&output=html) -- [Ion channels used by c. elegans](https://docs.google.com/spreadsheet/pub?key=0Avt3mQaA-HaMdEd6S0dfVnE4blhaY2ZIWDBvZFNjT0E&output=html) +- [The Virtual Worm (3D atlas of _C. elegans_ anatomy)](http://caltech.wormbase.org/virtualworm/) +- [The _C. elegans_ connectome (wiring diagram of neurons)](http://www.wormatlas.org/neuronalwiring.html) +- [Cell list of _C. elegans_](https://docs.google.com/spreadsheet/pub?key=0Avt3mQaA-HaMdGFnQldkWm9oUmQ3YjZ1LXJ4OHFnR0E&output=html) +- [Ion channels used by _C. elegans_](https://docs.google.com/spreadsheet/pub?key=0Avt3mQaA-HaMdEd6S0dfVnE4blhaY2ZIWDBvZFNjT0E&output=html) - [Database of Worm behavioral phenotypes](http://www.ncbi.nlm.nih.gov/pubmed/23852451) Currently our work on data collection and representation is divided among four subprojects: @@ -26,26 +26,26 @@ Currently our work on data collection and representation is divided among four s Below you can find information about each subproject, see the project’s current roadmap and access the associated data repositories -A lot of data about *C. elegans* is integrated into the model. In this project, we work on what forms we should put these data in to best leverage them for building the model. +A lot of data about _C. elegans_ is integrated into the model. In this project, we work on what forms we should put these data in to best leverage them for building the model. NeuroML Connectome ------------------ -Our computational strategy to accomplish this involves first reusing the *C. elegans* connectome and the 3D anatomical map of the *C. elegans* nervous system and body plan. We have used the NeuroML standard (Gleeson et al., 2010) to describe the 3D anatomical map of the *C. elegans* nervous system. This has been done by discretizing each neuron into multiple compartments, while preserving its three-dimensional position and structure. We have then defined the connections between the NeuroML neurons using the *C. elegans* connectome. Because NeuroML has a well-defined mapping into a system of Hodgkin-Huxley equations, it is currently possible to import the "spatial connectome" into the NEURON simulator (Hines & Carnevale 1997) to perform in silico experiments. +Our computational strategy to accomplish this involves first reusing the _C. elegans_ connectome and the 3D anatomical map of the _C. elegans_ nervous system and body plan. We have used the NeuroML standard (Gleeson et al., 2010) to describe the 3D anatomical map of the _C. elegans_ nervous system. This has been done by discretizing each neuron into multiple compartments, while preserving its three-dimensional position and structure. We have then defined the connections between the NeuroML neurons using the _C. elegans_ connectome. Because NeuroML has a well-defined mapping into a system of Hodgkin-Huxley equations, it is currently possible to import the "spatial connectome" into the NEURON simulator (Hines & Carnevale 1997) to perform in silico experiments. ### Previous accomplishments -- Building the *C. elegans* NeuroML file +- Building the _C. elegans_ NeuroML file ### Current roadmap ###[Updated NeuroML connectome model](https://github.com/openworm/OpenWorm/issues?milestone=15&state=open) -The [NeuroML connectome model](https://github.com/openworm/CElegansNeuroML) provides a framework for [multi-compartmental modeling](https://en.wikipedia.org/wiki/Multi-compartment_model) of the *C. elegans* nervous system. We are continuing to refine this to include more and more information that is known about the anatomy and dynamics of the nervous system in order to reach ever-improving biological realism. +The [NeuroML connectome model](https://github.com/openworm/CElegansNeuroML) provides a framework for [multi-compartmental modeling](https://en.wikipedia.org/wiki/Multi-compartment_model) of the _C. elegans_ nervous system. We are continuing to refine this to include more and more information that is known about the anatomy and dynamics of the nervous system in order to reach ever-improving biological realism. - [Create sample NeuroML connectome output](https://github.com/openworm/OpenWorm/issues/114) - [Remove Glutamate\_GJ etc in neuroConstruct project](https://github.com/openworm/OpenWorm/issues/50) -- [Create or reuse a NeuroML description of c. elegans motor neuron synapses](https://github.com/openworm/OpenWorm/issues/124) +- [Create or reuse a NeuroML description of _C. elegans_ motor neuron synapses](https://github.com/openworm/OpenWorm/issues/124) ### Issues list @@ -56,9 +56,9 @@ All issues related to [working with data](https://github.com/openworm/OpenWorm/i Repository | Description | Language ------------ | ------------- | ------------ -CElegansNeuroML | NeuroML based C. elegans model, contained in a neuroConstruct project | Java +CElegansNeuroML | NeuroML based C. elegans model, contained in a neuroConstruct project | Java Blender2NeuroML | Conversion script to bring neuron models drawn in Blender into NeuroML format | Python -NEURONSimData | Graphing voltage data from NEURON sims of C. elegans conectome | Python +NEURONSimData | Graphing voltage data from NEURON sims of C. elegans conectome | Python OWMeta | Metadata extraction, translation, storage, and sharing | Python @@ -76,7 +76,7 @@ With the ever increasing capacity to collect data about biological system, the n ### Current roadmap -- [Create a D3 implementation of the C. elegans connectome HivePlot](https://github.com/openworm/OpenWorm/issues/89) +- [Create a D3 implementation of the _C. elegans_ connectome HivePlot](https://github.com/openworm/OpenWorm/issues/89) ### Issues list @@ -86,6 +86,6 @@ All issues related to [working with data](https://github.com/openworm/OpenWorm/i Repository | Description | Language ------------ | ------------- | ------------ -wormbrowser | The Worm Browser -- a 3D browser of the cellular anatomy of the c. elegans | Javascript +wormbrowser | The Worm Browser -- a 3D browser of the cellular anatomy of the c. elegans | Javascript openwormbrowser-ios | OpenWorm Browser for iOS, based on the open-3d-viewer, which was based on Google Body Browser | Objective-C data-viz | Repository for scripts and other code items to create web-based visualizations of data in the project | Python From 038d93d5cef9a72f0ef1c7b76c44905896b3db7a Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Thu, 27 Jun 2024 17:55:24 +0100 Subject: [PATCH 06/16] Community: internal links updated --- docs/Projects/community-proj.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Projects/community-proj.md b/docs/Projects/community-proj.md index 73007458..d280e494 100644 --- a/docs/Projects/community-proj.md +++ b/docs/Projects/community-proj.md @@ -1,7 +1,7 @@ Community Outreach subproject ============================= -The effort to build the OpenWorm open science community is always ongoing. You can find out more about our OpenWorm community on [another page](../Community/community/). +The effort to build the OpenWorm open science community is always ongoing. You can find out more about our OpenWorm community on [another page](../community/). Previous accomplishments ------------------------ From 934b272cd9bd5f44f5ab2aeeb4805e433c5a0398 Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Thu, 27 Jun 2024 17:59:52 +0100 Subject: [PATCH 07/16] Community: internal url change --- docs/Projects/community-proj.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Projects/community-proj.md b/docs/Projects/community-proj.md index d280e494..773241be 100644 --- a/docs/Projects/community-proj.md +++ b/docs/Projects/community-proj.md @@ -1,7 +1,7 @@ Community Outreach subproject ============================= -The effort to build the OpenWorm open science community is always ongoing. You can find out more about our OpenWorm community on [another page](../community/). +The effort to build the OpenWorm open science community is always ongoing. You can find out more about our OpenWorm community on [another page](../../community/). Previous accomplishments ------------------------ From 56e5d4623424a780a84c5730975eb75f6a2ec272 Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Fri, 28 Jun 2024 11:48:12 +0100 Subject: [PATCH 08/16] mkdocs: adding c. elegans robots page --- mkdocs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/mkdocs.yml b/mkdocs.yml index b5552c82..91fdf1dc 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -20,6 +20,7 @@ nav: - Representation : Projects/datarep.md - Community Outreach : Projects/community-proj.md - Muscle / Neuron / Channel : Projects/muscle-neuron-integration.md + - C. elegans Robots : Projects/c-elegans-robot.md - Community: - Community Overview : community.md - GitHub : Community/github.md From 4ba61085f5b7f00f4c69dbb856eeebdf3e9b7dc5 Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Fri, 28 Jun 2024 11:58:47 +0100 Subject: [PATCH 09/16] Movement: link updates --- docs/Projects/worm-movement.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/Projects/worm-movement.md b/docs/Projects/worm-movement.md index 7fa83790..299439b7 100644 --- a/docs/Projects/worm-movement.md +++ b/docs/Projects/worm-movement.md @@ -55,7 +55,6 @@ Associated Repositories **Worm Tracker File Format Specification and Parser** - [https://github.com/openworm/tracker-commons](https://github.com/openworm/tracker-commons) -- [https://github.com/openworm/biological_data](https://github.com/openworm/biological_data) (placeholder repo to discuss worm video data) **André Brown's "Eigenworms" Code** @@ -65,6 +64,6 @@ Associated Repositories **Brown Lab Multiworm Tracking Code** -- [https://github.com/Behavioural-Genomics/tracking](https://github.com/Behavioural-Genomics/tracking) (not sure what this is, looks stale?) +- [https://github.com/Behavioural-Genomics/tracking](https://github.com/Behavioural-Genomics/tracking) (Closed) - [https://github.com/ver228/Multiworm_Tracking](https://github.com/ver228/Multiworm_Tracking) (Avelino Javer's work) - [https://github.com/KezhiLi/Tracking_Hypo](https://github.com/KezhiLi/Tracking_Hypo) (Kezhi Li's work; the computer vision code) From 6434adaf4c5505ceadb2f399b30cc267668d518c Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Fri, 28 Jun 2024 12:01:17 +0100 Subject: [PATCH 10/16] Datarep: removed unused section --- docs/Projects/datarep.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/Projects/datarep.md b/docs/Projects/datarep.md index c0a388f8..6df49694 100644 --- a/docs/Projects/datarep.md +++ b/docs/Projects/datarep.md @@ -88,4 +88,3 @@ Repository | Description | Language ------------ | ------------- | ------------ wormbrowser | The Worm Browser -- a 3D browser of the cellular anatomy of the c. elegans | Javascript openwormbrowser-ios | OpenWorm Browser for iOS, based on the open-3d-viewer, which was based on Google Body Browser | Objective-C -data-viz | Repository for scripts and other code items to create web-based visualizations of data in the project | Python From e0f92217f11e9822fa014548236f17ef84033df3 Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Fri, 28 Jun 2024 12:14:56 +0100 Subject: [PATCH 11/16] MNIntegration: updated hyperlinks --- docs/Projects/muscle-neuron-integration.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/Projects/muscle-neuron-integration.md b/docs/Projects/muscle-neuron-integration.md index 30f644f9..99fdd124 100644 --- a/docs/Projects/muscle-neuron-integration.md +++ b/docs/Projects/muscle-neuron-integration.md @@ -4,9 +4,9 @@ Muscle-Neuron-Channel Integration High-level Overview ------------------- -The fidelity of OpenWorm to its biological counterpart, *C. elegans*, depends on the realism of its constituent parts, such as computationally-modelled cells. The internal dynamics of these cells are largely controlled by ion channels, so a biophysically-informed ion channel model will, in-turn, support a realistic model of the entire organism. +The fidelity of OpenWorm to its biological counterpart, _C. elegans_, depends on the realism of its constituent parts, such as computationally-modelled cells. The internal dynamics of these cells are largely controlled by ion channels, so a biophysically-informed ion channel model will, in-turn, support a realistic model of the entire organism. -Broadly speaking, the team for this project will develop a workflow and tools to simulate *C. elegans* cell dynamics using simulated ion channel (*intracellular*) dynamics. +Broadly speaking, the team for this project will develop a workflow and tools to simulate _C. elegans_ cell dynamics using simulated ion channel (*intracellular*) dynamics. [![image](http://docs.google.com/drawings/d/1WzHYpgHZBDvbAxIb-KDDw0OatI8KWXQ8h_BeMVaQ2wM/pub?w=1238&h=869)](https://docs.google.com/drawings/d/1WzHYpgHZBDvbAxIb-KDDw0OatI8KWXQ8h_BeMVaQ2wM/edit) @@ -63,7 +63,7 @@ ChannelWorm [The ChannelWorm subproject](https://github.com/VahidGh/ChannelWorm/) is, at a high level, a pipeline to convert ion channel *data* found in scientific papers into ion channel *models*. This pipeline involves: -1. [Identification](https://github.com/VahidGh/ChannelWorm/issues/10/) of papers with ion channel data. +1. [Identification](https://github.com/VahidGh/ChannelWorm/issues/) of papers with ion channel data. 2. Extraction of data from these papers, including figures, active parameters and tabular data. 3. [Digitization](http://channelworm.readthedocs.org/en/latest/digitization/) of figures, and more generally, converting this information into machine-readable form. @@ -129,7 +129,7 @@ Issues for OWMeta are tracked [on Github](https://github.com/openworm/OWMeta/iss Muscle Model ------------ -The [muscle model subproject](https://github.com/openworm/muscle_model/) is concerned with modelling and simulation at the *cellular* level, specifically attempting to simulate the electrical dynamics of a *C. elegans* body wall muscle cell. +The [muscle model subproject](https://github.com/openworm/muscle_model/) is concerned with modelling and simulation at the *cellular* level, specifically attempting to simulate the electrical dynamics of a _C. elegans_ body wall muscle cell. This depends on what happens in [ChannelWorm](#channelworm), since ion channel dynamics are integral to our simulation of membrane dynamics. @@ -176,7 +176,7 @@ Issues for the muscle model are tracked [on Github.](https://github.com/openworm c302 ---- -The [c302 subproject](https://github.com/openworm/CElegansNeuroML/tree/master/CElegans/pythonScripts/c302/) is an effort to simulate the connectome of *C. elegans*, which includes its 302 neurons. The neural dynamics will start out with biologically-unrealistic integrate and fire cells, and be replaced with incrementally more realistic dynamics, as tests pass. Like the musclemodel, dynamics of neurons depend on ion channel dynamics within the cells, and thus depend on the channelworm subproject. +The [c302 subproject](https://github.com/openworm/CElegansNeuroML/tree/master/CElegans/pythonScripts/c302/) is an effort to simulate the connectome of _C. elegans_, which includes its 302 neurons. The neural dynamics will start out with biologically-unrealistic integrate and fire cells, and be replaced with incrementally more realistic dynamics, as tests pass. Like the musclemodel, dynamics of neurons depend on ion channel dynamics within the cells, and thus depend on the channelworm subproject. ### Previous accomplishments From f0845d8401e025dce9beb303e364934b1bac6bd3 Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Fri, 28 Jun 2024 12:34:50 +0100 Subject: [PATCH 12/16] Community: fixing internal links --- docs/community.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/community.md b/docs/community.md index c1cf1ea3..27507e93 100644 --- a/docs/community.md +++ b/docs/community.md @@ -11,7 +11,7 @@ Feeling lost? Not uncommon in open source projects. In fact, there are [whole pa Contribution Best Practices --------------------------- -What do I work on? We outline the work we are doing in the project using [GitHub issues](https://guides.github.com/features/issues/). Therefore, in order to figure out what to help out on, you need to be able to check them out for yourself. One way is to use this documentation to find [a project](/projects/) you want to contribute to. +What do I work on? We outline the work we are doing in the project using [GitHub issues](https://guides.github.com/features/issues/). Therefore, in order to figure out what to help out on, you need to be able to check them out for yourself. One way is to use this documentation to find [a project](../projects/) you want to contribute to. ### Find tasks to work on @@ -33,15 +33,15 @@ You can initiate a conversation with us on [Slack](https://slack.com) channels t - [Muscle model](https://app.slack.com/client/T02EPNETZ/C40BEV91S) - [ChannelWorm](https://app.slack.com/client/T02EPNETZ/C40MMRWDQ) -Once you have identified an issue you want to work on from a [particular project](/projects/), please announce your intention to help out by commenting on the specific [GitHub issue](github/#contributing-and-resolving-issues). +Once you have identified an issue you want to work on from a [particular project](../projects/), please announce your intention to help out by commenting on the specific [GitHub issue](../Community/github/#contributing-and-resolving-issues). ### Using OpenWorm repos on GitHub -Making a contribution of code to the project will first involve [forking one of our repositories](/Community/github/#forking-github-repositories), making changes, committing them, creating a pull request back to the original repo, and then updating the appropriate part of documentation. +Making a contribution of code to the project will first involve [forking one of our repositories](../Community/github/#forking-github-repositories), making changes, committing them, creating a pull request back to the original repo, and then updating the appropriate part of documentation. An alternate way to contribute is to create a new GitHub repo yourself and begin tackling some issue directly there. We can then fork your repo back into the OpenWorm organization at a later point in order to bring other contributors along to help you. -More details on best practices using OpenWorm repos on GitHub are available on [a separate page](github/). +More details on best practices using OpenWorm repos on GitHub are available on [a separate page](../Community/github/). ### Creating organizing documents @@ -156,9 +156,9 @@ Want to get notified when new content goes live? [Subscribe to the channel](http #### Playlists - Status Updates - Biweekly updates from the OpenWorm team. -- Journal Clubs - Like journal clubs that meet in person, the OpenWorm journal clubs use discuss new discoveries, tools and resources related to neuroscience, *C. elegans*, computational biology and open source science. Journal clubs are posted to social media in advance for any to watch and recordings then become available on YouTube. Learn more about our [journal clubs](#journal-clubs). +- Journal Clubs - Like journal clubs that meet in person, the OpenWorm journal clubs use discuss new discoveries, tools and resources related to neuroscience, _C. elegans_, computational biology and open source science. Journal clubs are posted to social media in advance for any to watch and recordings then become available on YouTube. Learn more about our [journal clubs](#journal-clubs). - Data Team meetings - Learn more about our [team meetings](#team-meetings). -- Real *C. elegans* +- Real _C. elegans_ - Building Blocks Membership From 3e91eaabb7a351f177092e3f7ccefd2c9b7fb875 Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Fri, 28 Jun 2024 12:43:55 +0100 Subject: [PATCH 13/16] Community: final changes --- docs/community.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/community.md b/docs/community.md index 27507e93..41ed78c5 100644 --- a/docs/community.md +++ b/docs/community.md @@ -81,9 +81,9 @@ An example of an effective proposal is [available online](https://docs.google.co The [OpenWorm documentation](http://docs.openworm.org) is a searchable repository of knowledge we have assembled to help new users get oriented to the different areas of the project. When new contributions are made, it is important that they are incorporated into the appropriate part of the documentation. The GitHub repo for the OpenWorm documentation [is here](http://github.com/openworm/openworm_docs). An issues list for changes that we are working on to improve the documentation [is here](https://github.com/openworm/openworm_docs/issues). -When they are ready to consume by the general public, simulation engines, visualization environments, and data sets should be added to [the resources page](/Resources/resources/). +When they are ready to consume by the general public, simulation engines, visualization environments, and data sets should be added to [the resources page](../Resources/resources/). -Information about the goals, progress, and roadmap of current or proposed projects should be added to [the projects page](/projects/). +Information about the goals, progress, and roadmap of current or proposed projects should be added to [the projects page](../projects/). The docs use ["GitHub-flavored" markdown format](https://help.github.com/articles/github-flavored-markdown/). This makes writing for GitHub (where most of our code is stored) and writing the documentation seamless. Markdown is also more forgiving in its syntax than, say, ReSTructured text, which was used previously. @@ -143,7 +143,7 @@ Want to tag OpenWorm on a tweet? Use @openworm and share the love. ### Blog -[Our blog](http://blog.openworm.org) is hosted in Tumblr. +[Our blog](https://openworm.tumblr.com/) is hosted in Tumblr. Interesting in being a guest on our blog? We love hearing about what members of the OpenWorm community are doing. If you have something to share, contact us at to discuss. @@ -155,7 +155,7 @@ Want to get notified when new content goes live? [Subscribe to the channel](http #### Playlists -- Status Updates - Biweekly updates from the OpenWorm team. +- Status Updates - Frequent updates from the OpenWorm team. - Journal Clubs - Like journal clubs that meet in person, the OpenWorm journal clubs use discuss new discoveries, tools and resources related to neuroscience, _C. elegans_, computational biology and open source science. Journal clubs are posted to social media in advance for any to watch and recordings then become available on YouTube. Learn more about our [journal clubs](#journal-clubs). - Data Team meetings - Learn more about our [team meetings](#team-meetings). - Real _C. elegans_ From 469535ec3fbfb60dbc27cfdd520e31ba48ee2b69 Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Fri, 28 Jun 2024 12:58:37 +0100 Subject: [PATCH 14/16] CommunityGitHub: removing outdated articles --- docs/Community/github.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/docs/Community/github.md b/docs/Community/github.md index 165c8148..e1a0fea9 100644 --- a/docs/Community/github.md +++ b/docs/Community/github.md @@ -10,7 +10,7 @@ This page contains a list of repositories maintained by the OpenWorm project on Repositories ------------ -View the full current list [repositories](/Community/repositories/) of repositories on GitHub. +View the full current list [repositories](../Community/repositories/) of repositories on GitHub. Accessing GitHub ---------------- @@ -84,10 +84,9 @@ Gist is a simple way to share snippets and pastes with others. All gists are Git How to: -- [Create Gists](https://help.github.com/articles/creating-gists) -- [Embed, Download and Copy Gists](https://help.github.com/articles/embedding-downloading-and-copying-gists) +- [Create Gists](https://docs.github.com/en/get-started/writing-on-github/editing-and-sharing-content-with-gists/creating-gists) +- [Fork and Clone Gists](https://docs.github.com/en/get-started/writing-on-github/editing-and-sharing-content-with-gists/forking-and-cloning-gists) -Read the [latest news and updates](https://github.com/blog/search?page=1&q=gis) on Gists at GitHub. Creating or Adding New Repositories ----------------------------------- From 2289888de2ea1d1265b56ef809568676d3550487 Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Fri, 28 Jun 2024 13:11:10 +0100 Subject: [PATCH 15/16] FAQ: hyperlink updates --- docs/faq.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/faq.md b/docs/faq.md index 695d076b..71741f82 100644 --- a/docs/faq.md +++ b/docs/faq.md @@ -71,7 +71,7 @@ In general, you won't step on any toes though -- multiple people doing the same ### Do you all ever meet up somewhere physically? -Subsets of us meet frequently, and there have been two meetings of the core OpenWorm team, one in [Paris in July 2014](http://blog.openworm.org/post/57193347335/community-updates-from-openworm-in-paris), and a second in London in Fall of 2014. We use Google+ hangout to meet face to face on a regular basis in general meetings and in standing meetings of the subprojects. +Subsets of us meet frequently, and there have been two meetings of the core OpenWorm team, one in [Paris in July 2014](https://openworm.tumblr.com/post/57193347335/community-updates-from-openworm-in-paris), and a second in London in Fall of 2014. We use Google+ hangout to meet face to face on a regular basis in general meetings and in standing meetings of the subprojects. OpenWorm simulation and modeling -------------------------------- @@ -108,7 +108,7 @@ It calculates a system of equations to produce a read out of the changing membra ### What is the connection between the basic proporties of _C. elegans_ neurons and human neurons? -C.elegans neurons do not spike (i.e. have [action potentials](http://en.wikipedia.org/wiki/Action_potential)), which makes them different from human neurons. However, the same mathematics that describe the action potential (known as the [Hodgkin-Huxley model](http://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model)) also describe the dynamics of neurons that do not exhibit action potentials. The biophysics of the neurons from either species are still similar in that they both have [chemical synapses](http://en.wikipedia.org/wiki/Chemical_synapse), both have [excitable cell membranes](http://en.wikipedia.org/wiki/Cell_membrane), and both use [voltage sensitive ion channels](http://en.wikipedia.org/wiki/Voltage-gated_ion_channel) to modify the [electrical potential across their cell membranes](http://en.wikipedia.org/wiki/Membrane_potential). +_C.elegans_ neurons do not spike (i.e. have [action potentials](http://en.wikipedia.org/wiki/Action_potential)), which makes them different from human neurons. However, the same mathematics that describe the action potential (known as the [Hodgkin-Huxley model](http://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model)) also describe the dynamics of neurons that do not exhibit action potentials. The biophysics of the neurons from either species are still similar in that they both have [chemical synapses](http://en.wikipedia.org/wiki/Chemical_synapse), both have [excitable cell membranes](http://en.wikipedia.org/wiki/Cell_membrane), and both use [voltage sensitive ion channels](http://en.wikipedia.org/wiki/Voltage-gated_ion_channel) to modify the [electrical potential across their cell membranes](http://en.wikipedia.org/wiki/Membrane_potential). ### What is the level of detail of the wiring diagram for the non-neuron elements? @@ -144,7 +144,7 @@ Single compartment models lack sufficient detail to capture the detailed shape o ### What is NeuroML and what does it represent? -An introduction to NeuroML is available [on their website](http://neuroml.org/introduction.php). In short, it is an XML based description of biological descriptions of neurons. +An introduction to NeuroML is available [on their website](https://neuroml.org/). In short, it is an XML based description of biological descriptions of neurons. ### How is excitation and inhibition in neurons handled in OpenWorm? @@ -175,7 +175,7 @@ OpenWorm code reuse ### What are LEMS and jLEMS? -[LEMS (Low Entropy Model Specification)](http://lems.github.io/jLEMS/) is a compact model specification that allows definition of mathematical models in a transparent machine readable way. [NeuroML 2.0](http://www.neuroml.org/neuroml2.php) is built on top of LEMS and defines component types useful for describing neural systems (e.g. ion channels, synapses). [jLEMS](https://github.com/LEMS/jLEMS) is the Java library that reads, validates, and provides basic solving for LEMS. A utility, [jNeuroML](https://github.com/NeuroML/jNeuroML), has been created which bundles jLEMS, and allows any LEMS or NeuroML 2 model to be executed, can validate NeuroML 2 files, and convert LEMS/NeuroML 2 models to multiple simulator languages (e.g. NEURON, Brian) and to other formats. +[LEMS (Low Entropy Model Specification)](http://lems.github.io/jLEMS/) is a compact model specification that allows definition of mathematical models in a transparent machine readable way. [NeuroML 2.0](https://docs.neuroml.org/Userdocs/NeuroMLv2.html) is built on top of LEMS and defines component types useful for describing neural systems (e.g. ion channels, synapses). [jLEMS](https://lems.github.io/LEMS/) is the Java library that reads, validates, and provides basic solving for LEMS. A utility, [jNeuroML](https://github.com/NeuroML/jNeuroML), has been created which bundles jLEMS, and allows any LEMS or NeuroML 2 model to be executed, can validate NeuroML 2 files, and convert LEMS/NeuroML 2 models to multiple simulator languages (e.g. NEURON, Brian) and to other formats. ### What is OSGi and how is it being used? From 8e6f3dae2e4434cbff50db6ca49e02a40c4889af Mon Sep 17 00:00:00 2001 From: KaanS139 Date: Fri, 28 Jun 2024 15:12:28 +0100 Subject: [PATCH 16/16] Resources: updates --- docs/Resources/resources.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/Resources/resources.md b/docs/Resources/resources.md index e99179f8..80002fab 100644 --- a/docs/Resources/resources.md +++ b/docs/Resources/resources.md @@ -15,7 +15,7 @@ Geppetto is a generic multi-algorithm integration platform written in Java and H More information on running Geppetto is [available online](http://geppetto.org). -[The project page for Geppetto](/Projects/geppetto/) has information about getting involved in its development with OpenWorm. +[The project page for Geppetto](../Projects/geppetto/) has information about getting involved in its development with OpenWorm. ### Sibernetic @@ -23,9 +23,9 @@ Sibernetic is the code base that currently implements the crawling model. Sibern ![image](http://i.imgur.com/KSWjCaW.jpg) -More information on running Sibernetic is [available online](http://sibernetic.org). +More information on running Sibernetic is [available online](https://openworm.org/sibernetic/). -[The project page for Sibernetic](/Projects/sibernetic/) has information about getting involved with its development. +[The project page for Sibernetic](../Projects/sibernetic/) has information about getting involved with its development. ### Connectome Engine and Lego Mindstorms robot @@ -80,8 +80,8 @@ that we have come across and adapted on Google Drive. ### C. elegans NeuroML model in NeuroConstruct -The NeuroML conversion of the [Virtual Worm Blender files](http://caltech.wormbase.org/virtualworm/) has been imported into a [neuroConstruct](http://www.neuroConstruct.org) project. [This page](/Resources/running-nc/) provides instructions for obtaining the latest version of neuroConstruct, getting the latest CElegans project and generating/visualizing the cells and connections. +The NeuroML conversion of the [Virtual Worm Blender files](http://caltech.wormbase.org/virtualworm/) has been imported into a [neuroConstruct](http://www.neuroConstruct.org) project. [This page](../Resources/running-nc/) provides instructions for obtaining the latest version of neuroConstruct, getting the latest CElegans project and generating/visualizing the cells and connections. ![CElegansnC](https://github.com/openworm/CElegansNeuroML/raw/master/CElegans/images/CElegans_nC.png) -More information about working with the data within it and other data entities can be found on the data representation project page \. +More information about working with the data within it and other data entities can be found on the data representation [project page](../Projects/datarep/)