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