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COPASI Website

This repository is the source for the COPASI Website. You can edit the pages directly in this github repository.

Each page is located in its own directory which contains the index.html file and supporting files like attachments or images. The index.html file contains the html content plus the Front Matter. The Front Matter provides information for the jekyll page generator, which is triggered on any commit to the master branch of this repository. It is possible to replace the index.html file with an index.md file which uses Markdown instead of html.

You can also clone:
    git clone git@github.com:copasi/copasi.github.io.git
this repository and edit and create pages in your local computer. In order to preview the pages you need to install jekyll. To create the pages and preview them on your local machine execute:
    bundle exec jekyll serve
You publish your changes by commiting and pushing them to the repository

Front Matter

This COPASI Website makes use of the following values in the Front Matter

---
layout:    default | structure | post
title:     The title of the page
section:   The menu section which shall be higlighted
structure: The structure to which the page belongs (optional)
---

Creating News Items

The news items are located in the _post directory. The file name convention is:

YYYY-MM-DD-[topic].(md|html)

where topic is one of COPASI, Release, Meetings, Media, or Collaboration. The front matter for a post is:

---
layout: "post"
title:  "Your title here"
author: "Your name"
topic:  "COPASI"
date:   "YYYY-MM-DD hh:mm:ss"
---

Adding Mathematical Formulas

To add mathematical formulas we can use the full LaTeX syntax. For LaTeX to be rendered correctly you will have to add the following to the front matter:

use_math: true

Publications citing COPASI

The list of publications of COPASI is kept in _data/articles/db.yml which is a YAML database. The data for each reference may contain the following fields, where lines starting with a minus may be repeated to supply multiple Keywords, Locations, or Funding sources:

-
 Reference:
 URL:
 Year:
 Keywords:
  - 
 Locations:
  - Institution, City, Country
 Funding: 
  -

Each entry in the file must start with a line including only a single '-'. Indentation is crucial and must be as in the example below.

-
 Reference: "Diao T, Pun D, Stahl SS (2013) Aerobic Dehydrogenation of Cyclohexanone to Cyclohexenone Catalyzed by Pd(DMSO)2(TFA)2: Evidence for Ligand-Controlled Chemoselectivity. J. Am. Chem. Soc. 135:8205-8212"
 URL: https://doi.org/10.1021/ja4031648 
 Year: 2013
 Keywords:
  - Chemistry
 Locations:
  - University of Wisconsin, Madison WI, USA
 Funding: 
  - NIH
  - NSF
-
 Reference: "Firczuk H, Kannambath S, Pahle J, Claydon A, Beynon R, Duncan J, Westerhoff H, Mendes P, McCarthy JEG (2013) An in vivo control map for the eukaryotic mRNA translation machinery. Molecular Systems Biology 9:635"
 URL: https://doi.org/10.1038/msb.2012.73
 Year: 2013
 Keywords:
  - Macromolecular biochemistry
 Locations:
  - University of Warwick, Warwick, UK
  - University of Manchester, Manchester, UK
  - University of Liverpool, Liverpool, UK
  - Virginia Tech, Blacksburg VA, USA
 Funding: 
  - BBSRC
-
 Reference: "Sier JH (2015) Investigation of the impact of MRP3 and MRP4 on the disposition of drugs and conjugates in rat and human. Doctoral thesis, University of Surrey."
 URL: http://epubs.surrey.ac.uk/id/eprint/807179
 Year: 2015
 Keywords: 
  - Physiology
 Locations:
  - University of Surrey, Guildford, UK