## SysMIC: a comprehensive online course in systems biology

The SysMIC course teaches the mathematics and computational methods used in systems biology.

It is funded by the BBSRC as a resource for members of its research community: from graduates beginning their career through to established researchers wishing to improve their skills.

The course syllabus is described here.

The course will open in January 2013.

enquiries @ sysmic.ac.uk

## custom latex macros in matjax

Our online textbook is generated from tex. MathJax is used to display equations but does not process all of the tags used in latex. In particular our equations include some \vspace and \index and \footmarknote commands.

There are two ways to deal with this:
1) process those commands and convert to xml tags then move them outside the mathjax equation
2) Tell MathJax to ignore the tags

For footnotes the first option needs to be done. However for the second we can add a MathJax config in our html script:

 MathJax.Hub.Config({ TeX: { Macros: { pounds: '{\\it\\unicode{xA3}}', index: ["{}",1], vspace: ["{}",1] } } }); 

The “1″s specify that the vspace and index commands take 1 argument.

UPDATE: I had a problem defining macros with asterisk / * in the name e.g. \vspace*
TO get around this I added a mathjax inline equation element in the html body.
\def\vspace*#1{} \def\vspace#1{}

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## Using chemical symbols in MathJax

The mhchem package will not be automatically loaded (c.f. other tex packages). This may let us have leftright harpoon arrows (we hope)
To include in MathJax add this to the configuration:

TeX: {
extensions: ["mhchem.js"]
}

then leftright harpoons etc can be used with \ce{CO2 + C <=> 2CO}

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## Optimising google search results II

sysmic.ac.uk has disappeared again from the google search results. One problem could be the multiple addresses allowed by parts of the site, e.g. our old address sysmic.cs.ucl.ac.uk still works.

To fix this I am going to look into a 301 redirect to direct all traffic to sysmic.ac.uk.

I also registered both sysmic.ac.uk and www.sysmic.ac.uk through googles webmaster tools portal. This enabled me to set the default domain to sysmic.ac.uk.

One thing I noticed was our indexed links. Google records 0 total indexed links. This indicates it has determined that our content is duplicated from somewhere else (possibly one of our alternative url names?) Hopefully google will correct this in a short time – otherwise I will investigate it further.

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Following our last SysMIC meeting there was some discussion about copyright, and I took some time to look into it.

In summary:
- our work is automatically copyrighted, adding a copyright symbol is not necessary but recommended (for enforcement in some foreign countries and to make it clear to others that you will act to protect your rights.)

- There is no fixed way to register materials to show you are the original author, and a court decides this on the evidence. In our case we have the SVN repository of our work which records the evolution of our documents, and I believe would be sufficient to prove we are the originating authors.

Below is some relevant material from the UK Intellectual Property Office.

Copyright is automatic in the UK and most of the rest of the world. It is a private right, so each copyright owner will usually have to make their own decisions about use of a copyright work and how to enforce their copyright.

Do I have to mark my work to claim copyright?
In some countries you must mark your work with the international © mark followed by your name and the year of creation. This is not necessary in the UK, but it may help you if you need to take action against someone using the work without your permission. Marking your work in this way also means
that you will get automatic copyright protection in certain foreign countries.
(You will get automatic copyright protection in many other countries even if you do not mark your work, but marking may still help).

How can I prove that my work is original?
Ultimately this is a matter for the courts to decide. But it may help if you:
• deposit copies of your work with a bank or solicitor; or
• send copies to yourself by special delivery (which gives a clear date stamp on the envelope), leaving the envelope unopened when it is returned to you.
Either of these methods could help to prove that your work existed at a certain time. (You can get more details of special delivery from post offices).

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## Useful tools for graph and network analysis

http://mavisto.ipk-gatersleben.de/

MAVisto includes tools for motif searching , and datasets in gml for

i) Transcriptional regulatory network of Escherichia coli
ii) transcriptional regulatory network of Saccharomyces cerevisae

This could be useful for making a example or teaching networks.

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## Browser compatibility

An issue that is very important is ensuring that users are able to access the feautres of the site. Most users on their own machines have the latest browsers (or can install them).

However university clusters often have older versions of browsers. (For instance the UCL cluster room has Firefox 3.6 / 4 and IE8). In particular these lack:

new html5 tags
svg support
input slider / spinner controls

In addition users browsing on mobile devices may see other problems with the site.

I don’t want to spend a lot of time patching the website so that older browsers work, but on the other hand it is important that the technologies and plugins on the site where possible can be used with odler browsers, and clear messages are displayed to users (or gracefull fallbacks) are in place.

Useful tools for doing this:

Run old versions of IE on Mac

http://osxdaily.com/2011/09/04/internet-explorer-for-mac-ie7-ie8-ie-9-free/

http://tumblr.jonthornton.com/post/11405634980/how-to-run-microsofts-ie-vpc-images-in-virtualbox

http://www.oldapps.com

Browser compatibility info:

http://caniuse.com

http://www.findmebyip.com/litmus/

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## converting svg to canvas and png

I was searching for a way to save svg as pictures e.g. png and came across this.
It links to the canvg library which can convert svg on the fly into canvas images.
This should help us disaply them on older browsers such as IE8.

One drawback is the loss of mouse events (I think?)

http://stackoverflow.com/questions/3975499/convert-svg-to-image-jpeg-png-etc-in-the-browser/3976034#3976034

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It would be great to rise up the google site rankings. Currently our main homepage sysmic.ac.uk isn’t in there at all, although the BBSRCs page about us is #1. (At least when I search it).

In order to do this SysMIC has a google webmaster account and we have set up and submitted a sitemap for the wordpress site using plugin:

Our aim should be for our main site page to be visible on the first page of google results by the time we have our launch event.

Ideas on how to do this:
All SysMIC contributers can add a link to the site through their university web page.
Host universities can add a link to SysMIC in the lists of research projects.
We can add more relevant public content onto the site. e.g. posting tutorials and applets which may be of use externally.

Any other ideas?

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## useful resource for latex symbols

http://detexify.kirelabs.org/classify.html

Lets you draw the symbol you are looking for and locates the latex code for it…

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