4 February 2008

Education for Biologists; Tools utilized by Biologists and Cores.

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Part II: Tools (David Sexton Introduction)

This discussion dovetails Part I as we want to discuss tools that enable biologists to perform analysis. Some tools investigated:

Interproscan [1] Galaxy [2] DS--played with this a little to glue workflows together. Seemed to do well in going to NCBI, do a blast, bring blast results back to workbench to do follow-on analysis. But it appears to be more of a tool for bioinformaticians than biologists. It still requires knowledge of each step than working de-novo. MR--good experience. groups have used it for large scale analysis. Some are even starting to put their own tools into it, adding them for a limited user audience, its good for large-scale analysis, especially comparisons between datasets (e.g. overlaps between datasets that refer to defined genomic regions with start and stop, such as ChIP-on-chip data with genome annotations)

Biomart [3] Geneious [4] BOSC [5] Emboss [6] Lax-- GCG is going away, lax has moved to emboss but the migration was hard as the biologists were used to the GCC GUI.

Taverna [7] : reliability is not that high. Recommended to bring web service in house. Requires lots of file passing, and if those files are large, this makes it very cumbersome. There could be some solutions to get around this. Lax was surprised when it worked without much effort AK: Most problems occur with web services not running: having a local copy of said web services is the easiest solution. I use a local copy of Soaplab as it is trivial to add EMBOSS applications (or any command line program with an ACD file) to Soaplab. Seahawk/BioMoby should make this easy as well but I have not tried. N.B. main snag is that all files are moved across the network, which makes working with large file sizes almost a no go. This may be fixed in taverna2. Also I have had problems with the taverna client on 64-bit linux systems but I have not tried hard enough to debug this.

Micro-Array tools:

Good site for general microarray links: [8]

BASE [9] DL--trying to create a database using (second version) from sweden. people can retrieve data from web and have a plugin to. Some folks on the list have tried it. TM4: [10]: Lax: multiple experiment viewer from TIGR--good for experimentalist. madmax has gone commercial--no longer open source.

Webarray? [11] a web based microarray tool wraps around bioconductor and mysql backend.

Carmaweb [12]

UCdavis uses R package mostly for analysis

SNP array analysis

chipmonk. [13] “A tool to visualize and analyze chip on chip array data. However, they only have certain genomes available in their database. Some have had good experience talk to author who has bee very good at incorporating additional genomes. However the Arabidopsis genome seems to be troublesome. AK--Simple but useful. Its simplicity has enabled a few users to get to grips with analysing their data without being too confused over multiple options. Author has been good in incorporating genome of interest (yeast).

Plink [14]. A whole genome association analysis toolset. Analyzes large scale chip arrays. Vanderbilt, Harvard Med uses it. Developed at MGH.

WASP [15] from vanderbilt is publicly available.

Dchip [16] --some good usage, some not. Can do some simple analysis.

Visualizing structures?

pymol--http://pymol.sourceforge.net/

AK--One of the tools of choice for our structural groups. Loads of powerful feature and well as the capability to generate publication quality figures.

MAGE and Kinemage: [17] from Duke. A web based tool to connect structure and display.

autodoc [18], is very good for docking calculations.