Merge pull request #109 from openworm/development

Multiple documentation/links fixes

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
 -----------------------------------

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                    
 ---                                              | ---

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
 ------------------------

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
 ------------ | ------------- | ------------
-<a href="https://github.com/openworm/CElegansNeuroML">CElegansNeuroML</a> | NeuroML based C. elegans model, contained in a neuroConstruct project  | Java
+<a href="https://github.com/openworm/CElegansNeuroML">CElegansNeuroML</a> | NeuroML based <em>C. elegans<em> model, contained in a neuroConstruct project  | Java
 <a href="https://github.com/openworm/Blender2NeuroML">Blender2NeuroML</a> | Conversion script to bring neuron models drawn in Blender into NeuroML format  | Python
-<a href="https://github.com/openworm/NEURONSimData">NEURONSimData</a> | Graphing voltage data from NEURON sims of C. elegans conectome | Python
+<a href="https://github.com/openworm/neuronal-analysis/tree/master/NEURONSimData">NEURONSimData</a> | Graphing voltage data from NEURON sims of <em>C. elegans<em> conectome | Python
 <a href="https://github.com/openworm/OWMeta">OWMeta</a> | 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 +86,5 @@ All issues related to [working with data](https://github.com/openworm/OpenWorm/i
 
 Repository | Description | Language
 ------------ | ------------- | ------------
-<a href="https://github.com/openworm/wormbrowser">wormbrowser</a> | The Worm Browser -- a 3D browser of the cellular anatomy of the c. elegans | Javascript
+<a href="https://github.com/openworm/wormbrowser">wormbrowser</a> | The Worm Browser -- a 3D browser of the cellular anatomy of the <em>c. elegans<em> | Javascript
 <a href="https://github.com/openworm/openwormbrowser-ios">openwormbrowser-ios</a> | OpenWorm Browser for iOS, based on the open-3d-viewer, which was based on Google Body Browser | Objective-C
-<a href="https://github.com/openworm/data-viz">data-viz</a> | Repository for scripts and other code items to create web-based visualizations of data in the project | Python

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.
 

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