http://lane.stanford.edu/howto/index.html?id=_2419 A review of biotools you should know about, as recommended by the Lane Library's Bioinformationist, Dr. Yannick Pouliot en-us Produced by Lane Bioresearch Informationist, copyright 2007 The Board of Trustees of The Leland Stanford Junior University http://lane.stanford.edu/howto/index.html?id=_3457 Fri, 2 May 2008 10:52:00 -0700 AGEMAP is a database of microarray-based gene expression measurements that tracks changes in expression levels during the lifetime of the C57BL/6 mouse. http://lane.stanford.edu/howto/index.html?id=_3391 Fri, 18 Apr 2008 15:50:00 -0700 NextBio provides a truly novel, unified interface for researchers to easily formulate and test new hypotheses across vast collections of experimental data. http://lane.stanford.edu/howto/index.html?id=_3231 Fri, 08 Feb 2008 13:50:00 -0700 Aligning genomic DNA sequences for comparative genomics purposes requires accuracy and can be very time consuming. The LAGAN tools are well-suited for this purpose. http://lane.stanford.edu/howto/index.html?id=_3142 Tue, 22 Jan 2008 10:40:00 -0700 With this version of SciFinder, you no longer need to install the SciFinder desktop client to access CAS' vast databases! http://lane.stanford.edu/howto/index.html?id=_3050 Fri, 30 Nov 2007 15:13:00 -0700 OBRC is a comprehensive database of bioinformatics tools that also provides curated descriptions of each tool, for those times when you have no idea what tools might be applicable to your research problem. http://lane.stanford.edu/howto/index.html?id=_2974 Mon, 31 Oct 2007 14:13:00 -0700 DDD is an easy-to-use transcriptomic analysis system whose elegant interface emulates the dot blot technique. A nice way to compare your microarray results against those of sequencing-based transcript profiling. http://lane.stanford.edu/howto/index.html?id=_2833 Mon, 24 Sep 2007 15:20:00 -0700 Looking for a highly reliable survey of the genomic properties of a meaningful sample of the human genome? ENCODEdb is your source. http://lane.stanford.edu/howto/index.html?id=_2807 Mon, 17 Sep 2007 09:01:00 -0700 Want to quickly determine the membrane properties of your protein, and perhaps its subcellular localization? Try the LOCATE database for quality computational predictions. Mouse proteins only, but still useful if you've got a homologous protein. http://lane.stanford.edu/howto/index.html?id=_1392 Fri, 24 Aug 2007 19:30:00 -0700 Trying to correlate gene expression data with anatomy or developmental stage? Make sure you start with NCBI's Probe database. This highly queryable repository of reagents for functional genomics is an amazing way to quickly identify many different kinds of probes, the tissues in which they hybridize and images of their hybridization profiles. http://lane.stanford.edu/howto/index.html?id=_2697 Mon, 30 Jul 2007 17:00:00 -0700 Working with transcription factors? Make sure you start with BIOBASE's TRANSFAC, preferably the Professional version. This database is your best source of transcription factor data carefully curated from the literature. http://lane.stanford.edu/howto/index.html?id=_2653 Thu, 12 Jul 2007 14:00:00 -0700 Can't afford Ingenuity Pathways Analysis (IPA)? Want to run your own IPA-like analyses on your local computer? Have a look at the Database for Annotation, Visualization and Integrated Discovery (DAVID), a powerful publicly accessible microarray analysis system. http://lane.stanford.edu/howto/index.html?id=_2548 Mon, 11 Jun 2007 10:35:00 -0700 Do you use Ingenuity Pathways Analysis? If so, here's an opportunity to learn from other users at Stanford. Who are they? How are they using IPA? What problems have they encountered and how were they resolved? http://lane.stanford.edu/howto/index.html?id=_2459 Fri, 01 Jun 2007 20:35:00 -0700 CDTree is an excellent tool for understanding the diversity of sequences that make up a conserved protein domain, identifying which residues may confer unique properties, and understanding how these sequences have diverged from each other, both in the same species (paralogs) and across species (orthologs). http://lane.stanford.edu/howto/index.html?id=_1906 Mon, 08 May 2007 17:00:00 -0700 SAM is an Excel add-in for estimating the number of microarray chips required to reach a pre-defined level of significance of difference between the mean of scores from two different conditions, given a set of genes for which preliminary expression data is available . http://lane.stanford.edu/howto/index.html?id=_2459 Mon, 07 May 2007 18:00:00 -0700 CDTree is a powerful integrated suite of software tools for analyzing and visualizing sequences from protein domains in NCBI's Conserved Domains Database (CDD) in the context of domain family hierarchies. You can even align your own sequences against these domains and see how they differ. http://lane.stanford.edu/howto/index.html?id=_2444 Tue, 1 May 2007 15:00:00 -0700 TranscriptionDetector is a program for detecting transcripts based on signals from whole-genome tiling microarrays probes, and doing so in statistically robust manner. http://lane.stanford.edu/howto/index.html?id=_2433 Mon, 30 Apr 2007 14:00:00 -0700 GENEVAR is a unique dataset of genome-wide microarray-based gene expression measurements obtained from the samples that were used to construct the Haplotype Map, thus enabling an understanding of gene expression in a genetically-characterized background. http://lane.stanford.edu/howto/index.html?id=_2336 Fri, 27 Apr 2007 14:00:00 -0700 LaneConnex now makes it possible to launch searches of the Lane Library's resources right from your browser's search box. if you're using FireFox 2.0 or Internet Explorer 7.0 or above, search plugins (extensions) are available for these browsers. See full article for easy installation steps.