Merge pull request #105 from KaanS139/master

Edits to Openworm_doc website

.github/workflows/mkdocs.yml

@@ -84,6 +84,6 @@ jobs:
             git add last_build_sha
             mv $REPO_METADATA_SHAS.temp $REPO_METADATA_SHAS
             git commit --amend -m "Deploy master@$SHA [ci skip]"
-            git remote set-url origin https://${{ github.token }}@github.com/openworm/openworm_docs.git
+            git remote set-url origin https://${{ github.token }}@github.com/${{ github.repository_owner }}/openworm_docs.git
             git push -f origin gh-pages
         fi

docs/Projects/sibernetic.md

@@ -1,7 +1,7 @@
 NeuroMechanical Modeling - Sibernetic
 =====================================
 
-While our ultimate goal is to simulate every cell in the c. Elegans, we are starting out by building a model of its body, its nervous system, and its environment. [Sibernetic](http://sibernetic.org) is the home of the C++ code base that implements the core of the model. We have implemented an algorithm called Smoothed Particle Hydrodynamics (SPH) to simulate the body of the worm and its environment using GPUs. This algorithm has been initially worked out in C++ (with OpenGL visualization).
+While our ultimate goal is to simulate every cell in the c. Elegans, we are starting out by building a model of its body, its nervous system, and its environment. [Sibernetic](https://openworm.org/sibernetic/) is the home of the C++ code base that implements the core of the model. We have implemented an algorithm called Smoothed Particle Hydrodynamics (SPH) to simulate the body of the worm and its environment using GPUs. This algorithm has been initially worked out in C++ (with OpenGL visualization).
 
 To get a quick idea of what this looks like, check out the [latest movie](https://www.youtube.com/watch?v=SaovWiZJUWY). In this movie you can see a simulated 3D c. elegans being activated in an environment. Its muscles are located around the outside of its body, and as they turn red, they are exerting forces on the body that cause the bending to happen.
 
@@ -14,11 +14,11 @@ Previous accomplishments
 Current roadmap
 ---------------
 
-### [Electrofluid Paper](https://github.com/openworm/OpenWorm/issues?milestone=17&state=open)
+### [Electrofluid Paper](https://github.com/openworm/OpenWorm/issues?milestone=17&state=closed)
 
-We are writing a manuscript focusing on the work we have to implement SPH in the project and apply it to muscle cells and the worm body. @vellamike, @a-palyanov and @skhayrulin are taking the lead on this,
+We are writing a manuscript focusing on the work we have to implement SPH in the project and apply it to muscle cells and the worm body. [@vellamike](https://github.com/vellamike), [@a-palyanov](https://github.com/a-palyanov) and [@skhayrulin](https://github.com/skhayrulin) are taking the lead on this.
 
-The proposal is to do this after the Sibernetic proof of concept worm wiggling is complete.
+The proposal is to do this after the Sibernetic proof of concept worm wiggling, both of which have since been completed.
 
 Issues list
 -----------

docs/background.md

@@ -6,9 +6,9 @@ History
 
 Established in January 2011, OpenWorm has since that time built a community of highly-motivated and highly-skilled individuals and coordinated their work. This community has produced scientific publications making use of scientific research published through open access, helping to show the validity of the open science approach we have taken.
 
-Please [visit here](fullhistory/) for a more extensive history of the project.
+Please [visit here](../fullhistory/) for a more extensive history of the project.
 
-More information is available on the past history of [OpenWorm releases](releases/).
+More information is available on the past history of [OpenWorm releases](../releases/).
 
 Why do this?
 ------------
@@ -21,10 +21,10 @@ Complex neuronal activity is the result of countless interactions between molecu
 
 We are building a simulation platform to prove it is possible to make good models of complex neuronal activity, starting with a digital worm. We are making the simulation platform open source because we believe anyone should be able to use it to understand how neurons and cells work.
 
-Why *C. elegans*?
+Why _C. elegans_?
 -----------------
 
-In the field of neuroscience, one of the simplest organisms that are studied is *Caenorhabditis elegans*, or *C. elegans* for short. It only has 302 neurons, has a very consistent lifecycle, and is well studied. Its whole body has only 1000 cells total. With those 1000 cells it solves basic problems of feeding, mate-finding, predator and toxin avoidance using a nervous system driving muscles on a body in a complex world.
+In the field of neuroscience, one of the simplest organisms that are studied is _Caenorhabditis elegans_, or _C. elegans_ for short. It only has 302 neurons, has a very consistent lifecycle, and is well studied. Its whole body has only 1000 cells total. With those 1000 cells it solves basic problems of feeding, mate-finding, predator and toxin avoidance using a nervous system driving muscles on a body in a complex world.
 
 The cells in its body work together to produce its behavior. Instead of starting with the behavior and building a simple system to capture it, we are starting with making models of the individual cells and their interactions. If we do this correctly so that the cells act on each other as they do in the real organism, we will have a much more realistic model than we would get trying to go straight to the behavior.
 
@@ -72,7 +72,7 @@ The consequence of this from an engineering perspective is, in order to simulate
 
 ### Model optimization
 
-There are a lot of aspects of *C. elegans* that we will not be able to measure directly for a while based on experimental limitations. These are ["free parameters"](http://en.wikipedia.org/wiki/Free_parameter). The conventional wisdom on modeling is to minimize the number of free parameters as much as possible. Sometimes, the large number of free parameters are used as an argument to avoid making computational simulations.
+There are a lot of aspects of _C. elegans_ that we will not be able to measure directly for a while based on experimental limitations. These are ["free parameters"](http://en.wikipedia.org/wiki/Free_parameter). The conventional wisdom on modeling is to minimize the number of free parameters as much as possible. Sometimes, the large number of free parameters are used as an argument to avoid making computational simulations.
 
 In this case, we have to make do with what we have and make some good educated guesses about the free parameters. There is a [mathematical discipline that helps us do that known as optimization](http://en.wikipedia.org/wiki/Mathematical_optimization). For our purposes, you can think of this as generating many different versions of a model, each version with slightly different parameters, and then measuring if the model produces good results. If a model produces better results by changing the parameters in a particular way, you try to keep changing the parameters in that way and see if you get even better results. In this way, roughly speaking, optimization techniques enable scientists to turn a problem of lack of data into a problem that a computer can address using brute force calculations.