BIOINFORMATICS Bookmarks

ComparativeGenomics Phylo GigaScience | Full text | The 3,000 Rice Genomes Project Rice, Oryza sativa L., is the staple food for half the world’s population. By 2030, the production of rice must increase by at least 25% in order to keep up with global population growth and demand. Accelerated genetic gains in rice improvement are needed to mitigate the effects of climate change and loss of arable land, as well as to ensure a stable global food supply. Courses Bio 5495/BME 537: homework, week 12 Bioch508 - Syllabus A Guide to Molecular Sequence Analysis BioComputing Hypertext Coursebook Documentation and Bioinformatics Courses http://linkage.rockefeller.edu/wli/bioinfocourse.html Bio 5495/BME 537 Computational Molecular Biology a list of bioinformatics courses and degress worldwide CSE 590BI, Winter 1998 CSE 527, Winter 2000 Biology 68: 2001S Databases FlyBase @ flybase.bio.indiana.edu Generic Model Organism Database Construction Set BioWarehouse Software Overview Sequence Database Searching and Sequence Scoring Methods Tutorial Object-Oriented Databases Bioinformatics Institute MASC: an RHdb Query Tool bio.perl.org - Projects The Protégé Ontology Editor and Knowledge Acquisition System Home — DbNP Genetics linkage software list (page 1) MadMapper: genetic marker scores QC, grouping and inference of linear order HPC Progeniq HPCVL Industrial Technology Centre Home Page LIMS Symyx NCICB GForge: lpgLIMS: Project Info Markers MapDisto Genetics Software: Home Michelmore MadMapper: genetic marker scores QC, grouping and inference of linear order SNP day2_400pm_livingston.pdf (application/pdf Object) The Single Nucleotide Polymorphism Database (dbSNP) of Nucleotide Sequence Variation Gene Codes Sequencher 4.9 | SNP Hunting Tutorial linkage software list (page 1) xQTL workbench MSTMap -- an efficient tool for constructing genetic linkage maps QGene Metabolomics Pathway Tools Information Site PathVisio / WikiPathways Metagenomics MEGAN - Metagenome Analysis Software — Algorithms in Bioinformatics Phymm + PhymmBL :: Center for Bioinformatics and Computational Biology MG-RAST - Home RDP - Ribosomal RNA Classifier TreeLign: Automatic Update of 16s rRNA Phylogenetic Tree and Multiple Alignment in Metagenomics Multiple alignment Zucker, Mult. Alignment A Gentle Guide to Multiple Alignment Jalview alignment viewer STRAP - multiple sequence alignment: Interactive Editor STRAP Bioinformatics Lesson 4 -- Multiple Sequence Alignment Online Resources ISREC bioinformatics group WWW-server Profile Server MendelWeb Homepage The ProDom protein domain database The PCR Primers database Home Page Bioverse Biology Workbench Oxford Univ BioinformaticsCentre NXSensor http://galaxy.psu.edu/ Ontologies SSWAP Ontologies Ontologies by Keyword Pattern Recognition Bioinformatics & Pattern Discovery @ IBM / The Home of TEIRESIAS, MUSCA and DELPHI LogoBar - Java application for protein sequence Logos BioProspector ORegAnno: Open Regulatory Annotation Sequence logo | Facebook People & Programs Welcome to the BMERC, Computational Biology ( bioinformatics ), structure prediction, functional profiles, and genome analysis. Canada Bioinformatics Group Center For Applied Genomics Computational Biology and Informatics Laboratory at UPenn. INCOGEN Mendel Bioinformatics Group National Biotechnology Information Facility Bioinformatics Centre, University of British Columbia Bioinformatics Program Survey--Hemminger 2003 http://www.cs.usask.ca/projects/birl/birl.html Phylogeny TreeBASE Schema Distance UPGMA UPGMA Distance Methods Evolutionary relationships of human populations on a global scale -- Nei and Roychoudhury 10 (5): 927 -- Molecular Biology and Evolution NWREpaper_FINAL.pdf (application/pdf Object) Distance Methods weighbor.pdf (application/pdf Object) Bayesian Bayesian Phylogenetic Analysis Introduction to Bayesian phylogenetics — Agapow.net TreeView X Introduction to Phylogeny Phylogenetic Reconstruction Mesquite PAL: Phylogenetic Algorithms Library PhyML: fast, accurate estimation of large PHYlogenies by Maximum Likelihood Mavric: a python toolkit for phylogenetics PAUP* 4.0 TREEFINDER Vanilla PhyloGrapher Welcome Phylogeny-Tree search Proteins SCOP: Introduction amino acid colors Colors RasMol V2.6-beta-2 Reference Manual RasMol V2.7.5 Manual Amino acid colour schemes Colors and Color Schemes Install Details for KiNG ::: Kinemage Website Solve Puzzles for Science | Foldit RNA EteRNA | Played by Humans, Scored by Nature. Similarity The Statistics of PSI-BLAST Scores http://www.blc.arizona.edu/courses/wardbioinf/salign.html Biochemistry Research - Pearson Sequence Database Searching and Sequence Scoring Methods Tutorial Which matrix should I use? Weight Matrices for Sequence Similarity Scoring The Statistics of Sequence Similarity Scores Software The ARB project Apollo Genome Annotation Tool Index of /pub/ARB/ UVA Software Center The Sanger Centre : Informatics Software: Artemis The Sanger Centre : Wise2 Linux for Biotechnology CORBA: Linking Biological Databases CORBA for Beginners GeneCrunch - Genome Supercomputing genetic-programming.com-Home-Page Genome Workbench Home Page GP homepage Accelrys GCG—A comprehensive collection of sequence analysis tools INCOGEN IUBio Archive Java-based Molecular Biology Work Bench MatrixPlot MIRA - genome assembler PUMA (Production) The Sanger Centre : EMBOSS: The European Molecular Biology Open Software Suite SciGraphica Homepage - Scientific Graphics and Data Manipulation Working Objects Bioinformatics - Wikipedia, the free encyclopedia The Taverna Project Website Biolinux [ Home ] NTSys - Exeter Software Mfg DNA folding software DNAMAN bioinformatics software MIRA | Get MIRA at SourceForge.net UGENE - Integrated Bioinformatics Tools NetSci - Resources for Science in Drug Discovery Web Services and Grids Seqhound.usergroup Info Page Using Entrez Utilities Web Service with Apache Axis2 for Java BioMOBY BioMoby MOBY-S Client Initialization APSTC http://bioverse.compbio.washington.edu/rpc/ The Globus Toolkit GO Tutorial BMC Bioinformatics | Full text | Semantic similarity in the biomedical domain: an evaluation across knowledge sources Semantic similarity measures estimate the similarity between concepts, and play an important role in many text processing tasks. Approaches to semantic similarity in the biomedical domain can be roughly divided into knowledge based and distributional based methods. Knowledge based approaches utilize knowledge sources such as dictionaries, taxonomies, and semantic networks, and include path finding measures and intrinsic information content (IC) measures. Distributional measures utilize, in addition to a knowledge source, the distribution of concepts within a corpus to compute similarity; these include corpus IC and context vector methods. Prior evaluations of these measures in the biomedical domain showed that distributional measures outperform knowledge based path finding methods; but more recent studies suggested that intrinsic IC based measures exceed the accuracy of distributional approaches. Limitations of previous evaluations of similarity measures in the biomedical domain include their focus on the SNOMED CT ontology, and their reliance on small benchmarks not powered to detect significant differences between measure accuracy. There have been few evaluations of the relative performance of these measures on other biomedical knowledge sources such as the UMLS, and on larger, recently developed semantic similarity benchmarks. THE NEXT GENERATION OF SIMILARITY MEASURES THAT FULLY EXPLORE THE SEMANTICS IN BIOMEDICAL ONTOLOGIES (World Scientific) Databases | dbfetch | EMBL-EBI Alfred P. Sloan Foundation bio-computing links Bioinformatics.Org: Project Info BioWiki:Community Portal - BioWiki Gaggle GSC - Chinook University of Manitoba: Statistical reports for: /faculties/afs/plant_science/courses/PLNT7690/ University of Manitoba: Statistical reports for: /faculties/afs/plant_science/courses/PLNT7690/ Bioinformatics - recent issues Home : Statistics for Biologists A collection of articles from the publisher of Nature that discusses statistical issues biologists should be aware of and provides practical advice to improve the statistical rigor and reproducibility of their work.
bioLegato Simple Spreadsheet Spreadsheet (XMLmind XML Editor Java[tm] API) The Java(TM) Boutique - SpreadSheet.java

BIRCH paper Biolinux [ Home ] Bio-Linux BIOrpms EMBOSS Homepage EMBOSS: The Project Documents Kaptain 0.72 Kaptain - EMBOSS Pise http://galaxy.psu.edu/ The Taverna Project Website