genSpace

 

Active Projects »

Reducing Testing Overhead

Unit test virtualization: significantly reducing the time to setup unit tests

 

CS/SE Education

New Techniques and Approaches to improve CS/SE Education

 

Managing Sensitive Data on Mobile Devices

Supporting privacy requirements on mobile devices

 

Overcoming the Intuition Wall: Automatic Graphical Analysis of Programs to Discover and Program New Computer Architectures

A joint project encompassing computer architecture, machine learning and software engineering

 

An Open Software Framework for the Emulation and Verification of Drosophila Brain Models on Multiple GPUs

Software frameworks and tools to emulate fly brains

 

Software Testing for Non-Testable Programs

Automating metamorphic testing techniques at runtime

 

In Vivo Testing

Executing tests in the deployment environment, using the state of the running application

 

Societal Computing

Exploring the impact of computational tradeoffs on societal concerns such as Privacy, Green Computing, Sustainability, and Cultural Differences

 

ARIS

Automated Online Evaluation for Improving Cyber-Physical System Reliability

 

genSpace

Enabling collaboration support for users of the geWorkbench computational biology tool

 
 

About genSpace

 

geWorkbench (genomics Workbench) is 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 70 available plug-ins supporting the visualization and analysis of gene expression and sequence data. Example use cases include:

  • loading data from local or remote data sources.
  • visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
  • providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
  • validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.

genSpace is a suite of collaboration plugins to geWorkbench aimed to support knowledge sharing among computational biologists based on popular social networking motifs.  genSpace logs all user activities to a backend server, and data mines this information to recommends tools and workflows (sequences of analysis and visualization tools) in “people like you” style.  It also supports Facebook-like friends (direct collaborators) and networks (colleagues from same lab, institution or community), presence facilities including available/away/offline and live activity feed, and a shared research notebook that documents the details of all analyses.

This research is in collaboration with the Center for the Multiscale Analysis of Genomic and Cellular Networks (MAGNet) on the Columbia University Health Sciences campus, which is funded by NIH and NCI.

Team Members

Faculty

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

PhD Students
Fang-Hsiang (Mike) Su, mikefhsu [at] cs.columbia.edu

Former PhD Students and MS GRAs
Jon Bell, jbell [at] cs.columbia.edu
Swapneel Sheth, swapneel [at] cs.columbia.edu
Chris Murphy, cmurphy [at] cs.columbia.edu
Nikhil Sarda, ns2847 [at] columbia.edu

Former project students
Diana Chang
Anureet Dhillon
Gowri Kanugovi
Mayur Lodha
Koichiro Matsunaga
Lakshmi Nadig
Joshua Nankin
Cheng Niu
Gaurav Pandey
Hyuksoo Seo
Yuan Wang
Eric Schmidt
Nan Luo
Danielle Cauthen
Flavio Antonelli
Ning Yu
Jason Halpern
Evgeny Fedetov
Aditya Bir
Alison Yang

Links

Papers, Presentations, etc.

C2B2 retreat poster and slides, May 2013
C2B2 retreat poster and slides, May 2012
DEIT 2011 paper and slides – “Towards using Cached Data Mining for Large Scale Recommender Systems”
RSSE 2010 paper and poster – “The weHelp Reference Architecture for Community-Driven Recommender Systems”
C2B2 retreat posters (1 and 2), April 2010
SSE 2010 paper and workshop presentation – “weHelp: A Reference Architecture for Social Recommender Systems”
C2B2 retreat presentation and poster, March 2009
SoSEA 2008 paper and workshop presentation – “genSpace: Exploring Social Networking Metaphors for Knowledge Sharing and Scientific Collaborative Work”
C2B2 retreat presentation and poster, April 2008

Documentation
genSpace wiki
geWorkbench wiki
C2B2 project management wiki

Source Code
geWorkbench repository (login required)

 

Contact: Fang-hsiang (Mike) Su

Available student project positions:

Recommendation engine developer

geWorkbench is a software platform that provides various analysis tools in the domain of bioinformatics and computational biology. genSpace is a module that equips geWorkbench with social networking features including recommendation engine. We plan to develop our own recommendation mechanism/algorithm specifically for genSpace to provide analysis tool recommendations to users. 

What you will learn:

  1. Research experiences in recommendation system
  2. An industrial level system

Contact: mikefhsu@cs.columbia.edu

Web developer

geWorkbench is a software platform that provides various analysis tools in the domain of bioinformatics and computational biology. genSpace is a module that equips geWorkbench with social networking features including recommendation engine. We are working on developing mobile and web versions of genSpace. 

What you will learn:

  1. Development experiences in GWT(Vaadin) and Java-based web services
  2. An industrial level system 

Contact: mikefhsu@cs.columbia.edu

Mobile developer

geWorkbench is a software platform that provides various analysis tools in the domain of bioinformatics and computational biology. genSpace is a module that equips geWorkbench with social networking features including recommendation engine. We are working on developing mobile and web versions of genSpace. 

What you will learn:

  1. Development experiences in iOS, Android or Mobile web
  2. An industrial level mobile app

Contact: mikefhsu@cs.columbia.edu