AIPTASIA WIKI

  • Build a open resource for the bioinformatics community to access and contribute data and research on the aiptasia genome.
  • Create a tool for runnning tasks on the “BioInf” cluster from the internet.
  • Creating a “piping” tool to connect perl (and other language) scripts when running them on the BioInf cluster through the wiki.
  • Automatically adding results from processes on the BioInf to the wiki.

Wiki Implementation

  • Based on initial analysis or the task at hand and the available free wiki software, Mickey and Felix decided to base our project on the MediaWikihttp://www.mediawiki.org/wiki/MediaWiki software. We are going to speak to Greg to see if he will advise us otherwise.
I'm curious what benefits we'll enjoy using MediaWiki as opposed to DokuWiki? 
In particular, MediaWiki relies on MySQL rather than the native file system, 
which introduces another layer of complexity in installation, maintenance, 
and support. 
This is not to say I'm against exploring MediaWiki, but I am curious what 
attracted you guys to this wiki over DokuWiki in particular, or other wikis
in general.  :-)
-Marc
  • Greg will set up a virtual machine within the CS firewall for us to host a test wiki that we can modify experimentally. It will also be accessible outside CS through SSH tunneling. The wiki will need access to a file system. If we use MediaWiki, it will also require a MySql database.
  • Eventually we will need a more permanent location outside the firewall.

Wiki Structure

The top level of the Wiki category/page tree will break pages up into 4 basic types/categories.

  • Tool pages are directly linked to a script file. They are created when a user uploads a script file. They contain information on the script such as it's input, output and function. The code itself may even be displayed or linked to.
  • Data pages are directly linked to a data file. They are created when a user uploads a data file. Several Data pages may be group together if one set of data is split among several files. Data pages should contain information about how, where, and by whom the data was collected.
  • Result pages are automatically created when a process is run. The result is uploaded to the file system and a connected wiki pages is automatically generated containing information about what script and data were used to obtain this result. A user may edit this page to add comments about the result. Other than the fact that it is automatically generated, Result pages can be treated exactly as data pages.
  • Discussion category is an overarching category that describes all pages that are not implemented above. Basically any page that is not directly linked to a file that can be used by the processing system is grouped under discussion.

Wiki Modification

Tools, Data, and Results pages will need to be able to be directly linked to a file. This could be as simple as holding the file name as a piece of data on the page, or perhaps there is a better way to link the files to enforce that each page his an associated file.

The Processing Page

The major innovation of the Aiptasia wiki will be the processing page (better name?). This page will allow users to import any number of Data pages (this considers Results pages to be just another type of Data page). Then the user imports any number of Tool pages. The users orders the Tools in the order that they should be run on each other. Ideally the page will verify based on information from the Tool pages whether the output of one Tool is the same as the input to the next Tool in the pipe chain. On a button click, the page will run the script linked to the first Tool page on the data linked to all of the Data pages, and pass the result as input data to the script of the next Tool page. Each intermediate result should have the option of being saved as a result page, the final result will always be saved.

Database

Check out the Database.

Accomplishments

  • A Ruby on Rails server has successfully been interfaced with the wiki–it is possible to send data from a Rails interface into the AiptasiaWiki, automatically generating pages. It is currently running as a daemon and can be viewed from inside the CS department or through SSH.

Preliminary List of Data and Tools to consider

Tools

ORF Prediction
Blast/local alignment
Clustal/Global alignment
Tree-Building
MapToGenome http://www.ambystoma.org/Tools/mapToGenome/
Hmmer (http://hmmer.janelia.org/)
SNP Prediction?

Data

Aiptasia ESTs and Contigs
GenBank Aiptasia
GenBank ESTs?
Nematostella
GenBank Dinoflagellates
Symbiodinium ESTs
GenBank Apicomplexan and Ciliate
GenBank nr
Swissprot
Pfam
SMART
KEGG/GO?

AiptasiaWiki