Gene Wiki Overview

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Community 

general open research

See the attached document for an overall concept of our Gene Wiki idea.

Please login and add comments on your thoughts on this project. Type of feedback we're looking for:

  1. Would this feature be useful to you for in-silico drug design? E.g. If you're a malaria scientist, is this useful for malaria drug target identification or should we focus our efforts on another genome?
  2. Are you interested in reaching out to world-wide resources such as India to help with this work?
  3. Would you use this feature openly if it were deployed on The Synaptic Leap? Please explain if you think it should be deployed somewhere else.
  4. What is your specialty and how would you use this feature? E.g. what contributions would you make to a community driven drug development?
  5. Which feature do you think is most useful?
  6. Are there important other features that you want added in the first or second version of the tool?

The more comments the better - even if they're negative. I want some online brainstorming.

Cheers!

Community-based Gene Annotation

This project is not yet active.

Gene annotation is essential for the advance of research in Malaria. Thus, we believe that allowing the users of the Malaria community in TSL to input (in a structured manner) their collective knowledge of a protein/gene can only benefit basic research towards drug discovery against Malaria. The aim of this project is to provide such tools in a flexible manner so they can be extended to different genomes in the future. When the project will be open (sometime in early 2006), all TSL registered users will be able to annotate genes/proteins from the malaria genome.

To contribute to the project you need to register with TSL.

Gene Cards for the Malaria genome

This project is not yet active.

Gene annotation is essential for the advance of research in Malaria. However, the annotation of genes is collected in several databases and sometimes (more than desired), associating the entries of different databases is no trivial. The aim of this project is to provide a tool that collects information from different databases for all genes in a genome and presents a summarized version of the collected information, which includes all relevant links to the original sources. Eventually, as the projects advances, we plan to maintain a wiki version of the Gene Cards so that users can modify its content.

The Sali group at UCSF has collected data from several annotated sources of the Malaria genome. As of September 2005, the Malaria genome had 5,270 ORFs.

The used sources were:

  • NCBI at http://www.ncbi.nlm.nih.gov/
  • BioMart at http://www.biomart.org/
  • ModBase at http://www.salilab.org/modbase

You will be able to search the database from this page after the project is released in early 2006.

Gene Wiki Programmers Needed

Subject 

Request for Help

TDI and TSL are in need of volunteers for the tools development within the Malaria community. You can read about the projects themselves here. So, what we need? Basically, we seek programmers with an interest of being part of a new community for BioMedical research. You would be applying your skills to develop tools that that should help advance the research of drug discovery for neglected diseases. This is something that you will feel good about! Gives good Karma!! The skills we are looking for in a volunteer in those projects are: - JavaScripting (in particular bookmarklets) - PHP programmer - MySql database experience - Familiarity developing Wiki-based tools a strong plus. - Familiarity with Drupal a strong plus - Familiarity with Trac a strong plus - Familiarity with Subversion a strong plus If you see that you would like to join, please do so by posting a comment to this entry! Thanks! marc

Malaria Gene Basket

This project is in discussion.

Gene annotation is essential for the advance of research in Malaria. Thus, we believe that allowing the users of the Malaria community in TSL automatically "annotate" each gene/protein in the malaria genome, can only benefit basic research towards drug discovery against Malaria. The aim of this project is to provide such tools in a flexible manner so they can be extended to different genomes in the future.

As seen in other social communities for photos or bookmarks., TSL registered users will be able to save gene cards in their baskets and associate pieces of information or tags to entries in the basket. This will allow a semi-automatic association of data to particular genes in their baskets.

The mechanism will take advantage of the use of bookmarklets so that the user can add information to its basket with just one click on their browser.

For example, a user may be browsing the literature at PubMed and find an interesting article, with just one click the system should be able to propose and association between the article and any of the genes in his/her basket.

Target Selection for Structural Genomics of Malaria

This project is not yet active.

Structural genomics aims to structurally characterize most protein sequences by an efficient combination of experiment and modeling. Central to the success of these efforts is effective target selection. There are a variety of target selection schemes, ranging from focusing on only novel folds to selecting all proteins in a model genome. Many of the target selection strategies of the Structural Genomic Consortiums are biologically based, providing a set of protein targets that are key actors in an interesting biological process. This project aims to provide a flexible tool for general target selection (in this case of Structural Genomics) based on collective knowledge. TDI registered users can vote for genes/proteins that may be promissing candidates for structural determination. The aim of the project is to generate a list of target proteins, which structure may help the advance of drug discovery for malaria. Dr. Raymond Hui, from the Structural Genomics Consortium in Toronto, and Dr Marc A. Marti-Renom, a computational bioligist, from UCSF, will analyze the gene the community voted on to have the highest potential. Results from that analysis will be posted here as well as open-access databases such as PlasmoDB. To contribute to the project you need to register with TSL. We intend to release this project in the early month of 2006.