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SCF Bioinformatics & Biotech Library

PostPosted: August 15th, 2006, 8:40 pm
by Silkworm
This thread is intended to be a database for links pertaining to information covered by this sub-forum. Links to tutorials, videos, interactive media, etc. will be listed and categorized here. Please feel free to submit any additions for this library in this format:

Name of the Website, Link, 1 sentence description and then possibly a suggestion of what category (tutorials, videos, etc.) the link should go in.

Example:

The eSkeletons Project, http://www.eskeletons.org/, An interactive examination of primate morphology, Interactive Media

This is an example of how the link will be listed with the name of the contributor in parentheses at the end.

Interactive Media

The eSkeletons Project, http://www.eskeletons.org/. An interactive examination of primate morphology. (Silkworm)

Submissions will be listed by category on this particular post, which will be edited to serve as the SCF Bioinformatics & Biotech Library, a living document. And as it is living, it will change. Categories added and links added and removed as there is demand for it.

A few quick notes:

1.Please contribute your links. Our combined efforts will make this a valuable and comprehensive internet resource.
2.Please report broken links, make comments, here.
3.If you feel a site is at the apex of quality please endorse it. Recommended links will have a “*” added to them. These should not be taken lightly and only added to the best of the best.


SCF Bioinformatics & Biotech Library


Genomics

EcoGene, http://www.ecogene.org/index.php. An annotated E. coli genome. Updated daily. Includes links for E. coli forum, published articles for each gene (complete bibliography), specially formatted BLAST searches, CoLibri, PubMeds, etc. (graemhoek)

EMBL-EBI, http://www.ebi.ac.uk/embl/. The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) constitutes Europe's primary nucleotide sequence resource. (BioWizard)

National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease. (BioWizard, Cyndi Loo)

UCSC Genome Bioinformatics, http://genome.ucsc.edu/. This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE project. (BioWizard)

Organic Chemistry

See SCF Chemistry Library, http://www.sciencechatforum.com/bulletin/viewtopic.php?t=2296

Podcasts

Futures in Biotech, http://www.twit.tv/FIB. Hosted by Leo Laporte (from TechTV when it was still watchable).

Proteomics

Expasy Proteomics Server, http://ca.expasy.org. A host of online tools for protein sequence anaysis, motif searches, curated protein databases, and way more. (BioWizard)

Human Proteomics Initiavive, http://ca.expasy.org/sprot/hpi/. Provides - for each human protein - a wealth of information that includes the description of its function, domain structure, subcellular location, similarities to other proteins, etc. (BioWizard)

National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease. (BioWizard, Cyndi Loo)

Protein Data Bank, http://www.rcsb.org. The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. (BioWizard)

SWISS MODEL, http://swissmodel.expasy.org/SWISS-MODEL.html. SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists World Wide. (BioWizard)

PostPosted: August 18th, 2006, 1:15 pm
by BioWizard
Protein Data Bank, http://www.rcsb.org, The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease, Proteomics.

Expacy Proteomics Server, http://ca.expasy.org, a host of online tools for protein sequence anaysis, motif searches, curated protein databases, and way more, Proteomics.

Human Proteomics Initiavive, http://ca.expasy.org/sprot/hpi/, Provides - for each human protein - a wealth of information that includes the description of its function, domain structure, subcellular location, similarities to other proteins, etc..., Proteomics.

SWISS MODEL, http://swissmodel.expasy.org/SWISS-MODEL.html, SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists World Wide, Proteomics.

EMBL-EBI, http://www.ebi.ac.uk/embl/, The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) constitutes Europe's primary nucleotide sequence resource, Genomics.

NCBI Entrez, Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease, Genomics and Proteomics.

UCSC Genome Bioinformatics, http://genome.ucsc.edu/, This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE project, Genomics.

so

PostPosted: August 20th, 2006, 9:32 pm
by graemhoek
http://www.ecogene.org/

An annotated E. coli genome. Updated daily. Includes links for E. coli forum, published articles for each gene (complete bibliography), specially formatted BLAST searches, CoLibri, PubMeds, etc.

A very comprehensive tool for anyone doing research (esp. genetics) with E. coli.

IUPAC Naming software

PostPosted: August 22nd, 2006, 11:49 am
by graemhoek
http://www.acdlabs.com/download/iupacname.html

I wish I had this when I was taking orgo back in the day...

(NOTE FROM SILKWORM: Updated up to here)

Bioinformatics tools & databases

PostPosted: February 23rd, 2010, 9:09 pm
by Skar
An extensive database of bioinformatics tools. This database contains links to >2000 web based bioinformatics and software tools that are freely available to researchers. Please visit the following link to see the details: http://www.sciclips.com/sciclips/bio-protocols.do