Dynamics of ERK signaling pathways during L-LTP induction(Miningou et al 2021)

 Download zip file 
Help downloading and running models
Biochemical model of five signaling pathways (3 activated by cAMP and 2 activated by calcium) leading to ERK activation during L-LTP induction. Simulations show that calcium and cAMP work synergistically to activate ERK and that stimuli given with large inter-trial intervals activate more ERK than shorter intervals. Epac and RasGRF pathways contribute to early dynamics and PKA and CaMKII contribute to late dynamics of ERK activation.
1 . Miningou NT, Jedrzejewska-Szmek J, Blackwell KT (2021) Temporal pattern and synergy influence activity of ERK signaling pathways during L-LTP induction Elife [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Molecular Network;
Brain Region(s)/Organism: Hippocampus;
Cell Type(s): Hippocampus CA1 pyramidal GLU cell;
Gap Junctions:
Simulation Environment: NeuroRD;
Model Concept(s): Long-term Synaptic Plasticity; Stochastic simulation; Reaction-diffusion;
Implementer(s): Blackwell, Avrama [avrama at gmu.edu]; Jedrzejewska-Szmek, Joanna ;
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell;
1. Create account on github
2. Install git (if not already installed)
3. git clone https://github.com/neurord/D1pathways
4. Normal git stuff
5. Give me your github user name (to allow you to push)


Now, you can edit stuff.  Then
git status - tells you whether there are changes either staged for commit, or modified but not staged
git diff - use to verify or review your changes
git add - if a new file is created (instead of just editing existing files)
    can also be used to move an edited file to the staging area
git commit -a - use to stage and then commit changes (ready to upload)
    you will need to add a one line description of your change, and optionally a longer description
git push - upload your  changes and merge them with the existing version

git pull - to see changes to repository made by others

git commit specific_file_names - to avoid committing all files
git rm filename - to stage removing file from repository, needs to be followed by git commit

git log - to see the history of changes made to my local copy
git checkout filename - to pull just a single file from the repository
git reset --hard  - roll back to previous version of everything not committed.
ggit reset filename - just unstage one file
gitk& - a nice visual tool, sort of like eclipse, to show you the  various changes

git branch name -> to create a branch
you have to do something else for it to push to the repository

git branch -r -> to show remote branches (only on your computer
git branch -a -> to show both remote and local

git show branchname:filename -> to show the filename
git show branchname:filename > filenm will create a local copy, then you can copy stuff to a different branch
git checkout branchname --filename will overout/replace filename - easier, but less safe if you only want some things updatedg
git merge branchname - will replace all files from branch into your master branch - more automatic, but more dangerous.  best to commit or stash your changes first

then, to swich between branches (say you want to work on different branches0
git checkout otherbranch

now, you can make changes, commit, push them, then

git checkout master
this switches you back

after editing a branch, e.g. master, do the usual:
git  commit
git push
git checkout otherbranch (e.g. plasticity-rule)
git cherry-pick master -x

this will copy the files from the last master commit only and merge into plasticity-rule (other branch)
i.e. cherry-pick branch means take last commit from branch (that you are not working on) and merge into the branch you are working on

If you've made local changes, and forgot to pull first, then
git commit
git pull
git push

git stash
git pull
git stash apply or git pop
git stash drop - clears the last stash

wget url to download just a single file

git commit file
press enter
write msg
press esc
type wq
press enter

Loading data, please wait...