NEBC Software Documentation Pages
Categories include Bio-Linux 4.0, Bioinformatics Analysis, Other Bio-IT, Data Policy, FAQs, maxd, EST Analysis, Microarray Analysis, Agilent Technologies, Ontology Software, Bio-Linux 3.0, Bio-Linux 2.x and Microarray Data.
Bioinformatics Solutions from the NERC Environmental Bioinformatics Centre include tools and systems developed by the NEBC as well as other NEBC bioinformatics links.
“TIGR has many software systems available for free download. All of them are OSI Certified Open Source Software. Click on the links below to get more information about the various packages and to download the source code.
Microarray – MIDAS, MADAM, MEV, Spotfinder
Grid Computing – BLAST, HMMsearch, Panda, Genomic Assembly, Mummer
Sequencing / Finishing – AMOS, BAMBUS, AutoEditor, Assembler, Lucy
Alignment – MUMmer, AAT package
Gene Finding / Annotation – DAGchainer, MANATEE, PIRATE, PASA, GlimmerHMM, etc.,
Other – TGICL, TIGR McCoder, Schedulerâ€?
“The Sanger Institute is a genome research institute primarily funded by the Wellcome Trust. Our purpose is to further the knowledge of genomes, particularly through large-scale sequencing and analysis.�
Regulatory Sequence Analysis Tools
“Welcome to Regulatory Sequence Analysis Tools (RSAT). This site provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences. This web site is freely available for academic users. For users from commercial companies, please read our disclaimer.�
Mapping Bioinformatics Software, Genomic Applications, Gene Expression and Bioinformatics Software APIs from Canada’s Michael Smith Genome Sciences Centre. �The Genome Sciences Centre has a primary mandate to deploy resources and technology of a high-throughput genome mapping and DNA sequencing lab to decrypt the genetic code, specifically to advance cancer research, diagnosis and treatment.�
The EST Machine from the Telethon Institute of Genetics and Medicine, a “directory of links to selected bioinformatic resources for Expressed Sequence Tags analysis.�
Sequence Analysis Tools from the OUEST-genopole® bioinformatics center, which “aims at proposing innovative software in Bioinformatics. You will find here a very complete set of tools in bioinformatics, public databanks updated on a daily basis, and a range of links to seminars, training courses…â€?
Computational gene finding, genome assembly and large-scale genome alignment and other sequence analysis tools from CBCB. “The Center for Bioinformatics and Computational Biology is a joint effort between the College of Life Sciences and the College of Mathematical, Computer, and Physical Sciences, and is organized as a center within the University of Maryland Institute for Advanced Computer Studies (UMIACS).
Affiliated departments include Biology, Cell Biology and Molecular Genetics, Chemistry and Biochemistry, Computer Science, Entomology, Mathematics and Smith School of Business.�
“The NERC Environmental Bioinformatics Centre
Funded by the NERC Environmental Genomics and the Post-Genomics & Proteomics Thematic Programmes
Bioinformatics Solutions
The NEBC bioinformaticians work as a team to provide software solutions, bioinformatics and analysis consultation, training, and a customised computing platform for scientific research.
Tools and systems developed by the NEBC:
EST software: trace2dbest, PartiGene
Transcriptomics software: GeneSpring, maxd
Software is provided on a customised Linux system called Bio-Linux.
Other software tools developed by the NEBC: Software Projects
See a full list of bioinformatics software on the current version of Bio-Linux”
