... | ... | @@ -12,33 +12,29 @@ There are 2 different possibilities to simulate the whole model: |
|
|
|
|
|
**1. Merge**
|
|
|
As long as every module uses only ordinary differential or algebraic equations the modules can be merged to one big model.
|
|
|
*COPASI* can also handle some species stochastically using a hybrid solver.
|
|
|
[*COPASI*](http://copasi.org/) can also handle some species stochastically using a hybrid solver when simulating the exported SBML file.
|
|
|
|
|
|
**2. Consolidation**
|
|
|
The modules can also be simulated independently in the framework. The results of these independent simulations are consolidated in update steps at constant time intervals (0.1 s).
|
|
|
The modules can also be simulated independently in the framework. The results of these independent simulations are consolidated in update steps at constant time intervals (0.1 s suggested).
|
|
|
|
|
|
***
|
|
|
|
|
|
### Workflow
|
|
|
To facilitate the development of the YCM model, we use different places to store information and the used data types:
|
|
|
|
|
|
**1. Publications**
|
|
|
**Since June 2016:**
|
|
|
We use a [*Mendeley*](https://www.mendeley.com/) group for the YCM, you need a Mendeley account and an invitation to our group to use it.
|
|
|
|
|
|
**Before**
|
|
|
We use a [*CITAVI*](http://www.citavi.com/) project for all useful publication.
|
|
|
The project and the pdf files of the publications can be found in the folder:
|
|
|
**1. Publications**
|
|
|
We use a [*CITAVI*](http://www.citavi.com/) project for all used publications.
|
|
|
The project and the pdf files of the publications can be found locally in the folder:
|
|
|
*/basar/WCM/Refs/CITAVI/*
|
|
|
CITAVI runs on every computer (Windows server) and is free for everyone in the HU
|
|
|
|
|
|
**2. Framework & Model files**
|
|
|
On [**GitHub**](http://www.GitHub.com/):
|
|
|
Private repository using Git
|
|
|
*ssh://git@github.com:tbphu/ycm.git*
|
|
|
Invitation to *"tbphu"* and free [**GitHub**](http://www.GitHub.com/) account needed
|
|
|
On the GitLab server of the [TBP](https://rumo.biologie.hu-berlin.de/tbp/index.php) [GitLab](http://www.gitlab.com/) Server. Reached by [this link](https://ford.biologie.hu-berlin.de/YCM/).
|
|
|
|
|
|
Public repository using Git
|
|
|
*ssh://git@ford.biologie.hu-berlin.de:YCM/YCM.git*
|
|
|
|
|
|
To clone the repository, use `git clone git@github.com:tbphu/YCM.git`
|
|
|
To clone the repository, use `git clone git@ford.biologie.hu-berlin.de:YCM/YCM.git`
|
|
|
|
|
|
**3. Knowledge & information**
|
|
|
In this Wiki:
|
... | ... | @@ -50,11 +46,13 @@ In this Wiki: |
|
|
**The old [**WIKI**](http://wcmwiki.pbworks.com/) is no longer in use but still online!!**
|
|
|
|
|
|
**4. Data files**
|
|
|
All data files are stored in the YCM folder
|
|
|
All data files are stored internally in the YCM folder
|
|
|
*/home/basar/YCM/*
|
|
|
There are all tables, presentations and meeting hand-outs
|
|
|
The folder is read-only, but you can store files in the *./__add_items/* folder
|
|
|
They will be put into the best place =)
|
|
|
They will be put into the corresponding folders.
|
|
|
|
|
|
The YCM Database can be found at...
|
|
|
|
|
|
**Workgroup behaviour**
|
|
|
**Use naming schemes!**
|
... | ... | |