genSpace Project

Many researchers in the field of computational biology use the geWorkbench tool, a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 30 available plug-ins supporting the visualization and analysis of gene expression and sequence data, however it is purely a stand-alone application and does not have any collaboration capabilities.

This project, started in Fall 2007, is designed to develop proof-of-concept collaboration facilities suitable for inclusion in geWorkbench and, at least in principle, other plugin-based tool integration environments. The project aims to include a few of the well-known collaboration mechanisms, possibly including but not necessarily limited to instant messaging (as in AIM), social networking (as in Facebook), knowledge repositories (as in Usenet newsgroups) and shared folders (as in Webdav). However, only those existing collaboration mechanisms that will in some manner facilitate new research towards novel mechanisms will be chosen.

Some basic functionality has already been implemented: logging which analysis tools users run, the ability to log in to genSpace, rudimentary integration with the jClaim chat client, and a server-side instant messaging bot that allows for simple user interaction, such as the creation of social networks.

In Spring 2008, we integrated all of this functionality into an end-to-end system which allows all geWorkbench users to log into genSpace, communicate with other users, find experts on the tools they are using, and find other researchers who are similar to them. We also built visualization tools that allow users to see their social networks, and to see "collaboratively created workflows", which are automatically generated based on other users' activities.

A paper about our work was published at the Social Software Engineering and Applications (SoSEA) workshop colocated with ASE and is available here.

In Summer 2008, we began the development of a recommendation system in which genSpace can recommend actions based on what has been observed. We also implemented an admin user interface and performed further enhancement of some of the server-side features.

In Fall 2008, we implemented many new features which make use of our recommendation system. Users can view popular workflows which include or start with a particular tool. e.g., A user can choose to see all the workflows which involve ARACNE. Users can also view overall geWorkbench statistics such as the top 3 most popular tools of all time and the most popular workflows. We also added a Real Time Workflow Suggestion feature where genSpace provides real-time suggestions depending on the users's activities. e.g., If a user has run analysis A followed by analysis B, genSpace can suggest that the next best tool to use is C and that the historical superflows which start with A and B are A, B, C, D and A, B, C, F. In addition, users can now rate and comment on different tools and workflows. The users can rate the tools using the genSpace plugin in geWorkbench. The plugin also provides a link to a web application where users can read and post comments. The web application is written in PHP and Symfony.

This semester, we are looking to implement a user interface that allows users to perform such actions as joining social networks, seeing who is logged in, and getting advice and recommendations from the system. This would be integrated with geWorkbench and would serve as an alternative to using an IM client for working with social networks. We are also looking to understand the software engineering implications of retrofitting social networking capabilities onto standalone applications, e.g., caching, fault tolerance, privacy, etc.

Faculty
  Prof. Gail Kaiser, kaiser [at] cs.columbia.edu

Graduate Students
  Chris Murphy, cmurphy [at] cs.columbia.edu
  Swapneel Sheth, swapneel [at] cs.columbia.edu

Former members
  Diana Chang
  Anureet Dhillon
  Gowri Kanugovi
  Mayur Lodha
  Koichiro Matsunaga
  Lakshmi Nadig
  Joshua Nankin
  Cheng Niu
  Gaurav Pandey
  Hyuksoo Seo
  Jonathan Bell
  Yuan Wang
  Eric Schmidt