Summer 2006 Workshop

Watch this page for updates and tutorials about bioinformatics tools as researched by the MIBLab members.

Workshop Goals
In an effort to explore the state of the technology already available in bioinformatics, the BioMIB Lab team members have tried and tested a variety of existing tools for usability. The tools were selected based upon their relevance to the research currently in developement in the MIBLab. The tools were frankly critiqued based upon their design, features, ease of use and clarity for non-technical users. By dividing up these tools among the lab members and then presenting our findings, we hoped to impart on our entire team a condensed learning experience. Successes and downfalls of these tools were explored without every individual lab member taking the time to find, download, learn and sample each tool.

We present the results of our workshop here for others to review as a guide to these tools. Perhaps you will be able to more rapidly identify a tool that is of interest to you and to preview its style and usability. We hope that you benefit from our efforts and have the opportunity to more thoroughly appreciate the strong and varied tools that are available among the entire community of bioinformatics researchers.

Our inspiration for this workshop was derived from the efforts of the NCI and their devotion to open and integrated cancer research to speed us all towards the ultimate goal- a cure. We recommend visiting their website and learning more about the caBIG protocols.
 * caBIG

We highly recommend you listen to the [[Media:Carmona.ram|words of Surgeon General, Dr. Richard Carmona]], the keynote speaker at the spring 2006 caBIG Conference. We found it so inspiring that it was played at the start of our summer workshop to remind us all what we are striving for.

Databases
The ability to access, quickly and easily, the vast amount of clinical data already available can speed research and lower cost.
 * MicroArrays
 * ArrayExpress
 * caARRAY
 * GEO-Gene Expression Omnibus
 * Oncomine
 * Tissue
 * caIMAGE
 * Protein
 * BioGRID
 * Osprey
 * PIR-Protein Information Resource

Analysis
A variety of pre-existing algorithmic data processors can be invaluable to clinicians attempting to interpret results.
 * ARACNE
 * GenePattern
 * Gist
 * Tmm - Gene coexpression

Imaging
A picture is still worth a thousand words. The ability to create and interact with visual representations of experimental results can ease understanding.
 * Manipulation
 * VTK
 * Simulation
 * CellDesigner
 * CESE
 * E-cell
 * Virtual Cell
 * Interactions and Pathways
 * cMAP
 * Reactome

Management
Certain tools are simply needed to keep any lab organized, communicating and functioning comfortably
 * Wikis

Participants

 * Team 1
 * John Phan
 * Ben Bachman
 * Kiet Huyn
 * Kathy Pham
 * Jennifer Dale
 * Jeff Wang


 * Team 2
 * Todd Stokes
 * Xiao Randy Han


 * Team 3
 * Richard Moffitt
 * D. S.
 * Lauren Smalls-Mantey
 * Malcolm Thomas
 * JT Torrance


 * Team 4
 * Chang F Quo
 * Leang Chhun
 * Chanchala Kaddi
 * Tao Ma
 * Jorge Viveroz
 * Andrew Tantia


 * Team 5
 * Koon Yin Kong
 * Nishit Jain
 * Nikhar Kinger
 * Qaiser Chaundry
 * Sohaib Waheed


 * Support Team
 * Prof. May Wang
 * Pete Cutter
 * Susan Davis