Summer 2006 Workshop

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


Contents

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.


caBIG

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.

We highly recommend you listen to the 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.

Bioinformatics Tools

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
Personal tools