resource center::institute for computational biomedicine

Resource Center

The resource center is here to serve as a portal to useful information in computational biomedicine. New resources offered by the Institute or external sources are quickly introduced and links to further information are available for readers interested in a particular topic.

Bioinformatics Walk-in Clinics: To answer your bioinformatics questions, a member of the ICB will be available for consultation and advice every Monday between 2-4pm in the Weill Cornell Medical Library, in the Computer Room on the lower level.

[ services ]

Computational Research Tools

Microarray Resources

Consulting Services

Biocatalogs

Bioinformatics Infrastructure

Computational Genomics Core Facility

ICB Intranet

Mailing List

Computational Biology Service Unit at Cornell Univ. (Ithaca)

Weill Cornell Medical Library Bioinformatics Resources

[Note: The ICB intranet is available only to ICB personnel and requires username and password authentication]

[ tutorials and training ]

The institute offers workshops and tutorials for our bioinformatics resources. Please visit our education section for more information. We also offer individualized training. This is appropriate if you would like somebody in your lab to learn a specific bioinformatics method. The hourly fees for training are listed under our fee schedule.

[ tools developed at the ICB ]

Twease	Search MedLine at the Sentence level. Twease is a new web-based tool to search for information in MedLine. Twease indexes every word of Medline and offers innovative features which improve precision while maintaining a good level of recall. Check out the tutorials on Twease.org.
SigPath	A prototype of an information system to integrate qualitative and quantitative information about signaling networks.
Arcadia	A repository of mutants of GPCR and transporter proteins, and associated information.
Textractor	A software framework to support the development of tools that mine full text scientific articles to extract information.
TissueInfo	A series of tools and a curated database to predict the tissue distribution of genes and EST (knowledge-based prediction). TissueInfo can be applied to complete genomes and produces records suitable for data mining.
Crover	A software framework to support the development of Bioinformatics tools and applications.
RbDe	A web service allowing the iterative construction of residue-based diagrams of proteins. The constructed diagrams can be annotated to show experimental results (directed mutagenesis, accessibility, etc.) or to present key properties of the protein in the context of its secondary structure.
RbDg	RbDg is a program that generates residue-based diagrams of proteins. RbDg can be thought of as a batch version of RbDe with added features.
ProperTM	ProperTM is a web service that calculates properties associated with positions in a sequence alignment. The methods employed in this program are designed to analyze membrane proteins (and G-protein coupled receptors (GPCRs) in particular) but some of the options (i.e the calculation of a conservation index) could be useful for the analysis of sequences of non-membrane proteins too.
Real-time Experiment Control Software for Linux	A software system for scientific experimentation. Experimenters can use this system to design their own hard real-time data acquisition and control applications. Applications are split into two parts: the user interface and the real-time control module. The user interfaces are written as Qt C++ plugins which get loaded into the DAQSystem program. Real-time control modules, which use RTLinux or RTAI, are written as C code that gets loaded into the kernel and is executed by the rtlab.o kernel module.

News

Apr, 2009; The BDVal program developed by the Campagne laboratory for MAQC-II is now available from http://bdval.org. The software supports the development and evaluation of predictive biomarker models from high-throughput data. The web site offers binary and source distributions. [More]
Jan, 2009; Twease now supports searching MEDLINE articles by Author, Journal, and Publication Year. Examples for performing these searches can be found in the updated Twease tutorial. [More]
Jan, 2009; The free bioinformatics walk-in clinics are back and will be available every Monday, 2-4pm at the Weill Cornell Medical Library, in the Computer Room on the lower level. [More]

[News Archives] [Mailing List]

Events

Jul 7th; 1:00pm-2:00pm: Understanding Computation in Large Neuronal Networks - Yasser Roudi, Ph.D.; Nordic Institute for Theoretical Physics; LC-504 [Physiology and Biophysics Special Seminar]
Nov 1st: Sequencing of Individual Genomes: Impact on Society and Ethics ; Geneva, Switzerland [HUGO Symposium on Genomics and Ethics, Law and Society]

Bioinformatics links

National Center for Biotechnology Information
European Bioinformatics Institute
The Sanger Center
The Genome Database
The Institute for Genomic Research
Expert Protein Analysis System
Protein Data Bank
National Cancer Institute
Mouse Genome Informatics