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=4094 Mon, 18 Apr 2009 14:43:00 -0700 BOV is a nifty tool for visualizing BLAST sequence alignments using a Web browser. In addition to being flexible and easy to use, BOV's clean programming style and open source nature mean that it should receive particular consideration if customizations are necessary. http://lane.stanford.edu/howto/index.html?id=1333 Mon, 27 Apr 2009 9:53:00 -0700 PharmGKB, the primary repository of human pharmacogenetic data, has updated itself with an impressive new look and other functionality. http://lane.stanford.edu/howto/index.html?id=3932 Mon, 23 Feb 2009 18:21:00 -0700 Galaxy is an impressive metaserver for analyzing genomes without having to write custom programs. http://www.tictocs.ac.uk/ Wed, 18 Feb 2009 2:51:00 -0700 tiTOCs is a single, freely available source of RSS feeds for tables of contents from scientific journals. It's the best tool I know to rapidly find and subscribe to a TOS feed using RSS. http://lane.stanford.edu/howto/index.html?id=3888 Fri, 27 Jan 2009 12:05:00 -0700 Scriptome provides easy to use Perl scripts for running tedious file manipulation and data analysis. It's also a great way to learn how to program, right within the context of your task. http://lane.stanford.edu/howto/index.html?id=3858 Fri, 09 Jan 2009 17:42:00 -0700 ProPhylER visualizes the evolutionary constraints that have shaped a protein by displaying these constraints against its sequence, providing an effective way to quickly identifying regions of special significance. http://lane.stanford.edu/howto/index.html?id=3747 Fri, 30 Oct 2008 14:42:00 -0700 Bioinformatik Harvester generates a composite Web page from search results gathered from the main biological databases, providing an effective way to quickly understanding what the literature is saying about a protein of interest. http://lane.stanford.edu/howto/index.html?id=3640 Fri, 12 Sep 2008 14:42:00 -0700 If you've ever struggled with understanding an unfamiliar concept in bioinformatics, genomics, genetics or proteomics in a rapid manner, the Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics (EGGPB) is a great solution. http://lane.stanford.edu/howto/index.html?id=1168 Wed, 03 Sep 2008 14:24:00 -0700 The newly introduced BIOBASE Knowledge Library (BKL) is the successor to the venerable PROTEOME database. BKL provides dramatic improvements in interface design, including a new snazzy visualizer -- well worth using if your research involves proteins. http://lane.stanford.edu/howto/index.html?id=3344 Mon, 27 May 2008 14:24:00 -0700 GraphPad Prism is likely the easiest way to analyze statistical data up to a fairly high level of complexity. You can view the recently held class on GraphPad Prism here. http://lane.stanford.edu/howto/index.html?id=3470 Thu, 15 May 2008 13:24:00 -0700 e-Notebook, a component of the ChemBioOffice Ultra suite is very flexible and suitable for bioresearch, not just for chemists. 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.