We have developed or take advantage of a number of bioinformatics tools to facilitate our research
1) Est Express: a software suite for the automated analysis and annotation of sequencing projects. Developed by Robin Smith with the assistance of a number of lab members. BMC Bioinformatics. 2008 Apr 10;9:186. PMID: 18402700
2) Promolyzer: An unpublished extension of Est Express to identify known and potential transcription factor sites in genes.
3) HCS reports: A set of scripts, programs and plug-ins for Spotfire that automates the creation of quality control reports from HCS data from the Cellomics store. Developed by Willie Buchser.
4) Cellomics Store: API tool to export cell and well data: An unpublished tool that greatly facilitates exporting data from multiple plates from Cellomics Store to Spotfire. Developed by Willie Buchser.
5) Spotfire DecisionSite: Our favorite data visualization tool
6) Genego Metacore: Our favorite protein-protein interaction database
7) R and Octave: Programming languages used to model and analyze HCS data. Used by Omar Gutiérrez Arenas.
8) Magic Tool: A free program used to analyze microarray data. A great teaching tool. We have used it in our Developmental Neuroscience course and have written a manual that focuses on analyzing data from GEO.
9) Thermo Fisher Nautilus Laboratory Information Management System: Keeping track of the experiments and reagents in the lab is difficult but facilitated by using Nautilus.