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Useful Links

Material Safety Data Sheets (MSDS)

Online Material Safety Data Sheets are available from:

• New England Biolabs (each product description has a link to its MSDS). Searching or browsing our online catalog provides links to those product descriptions, or you can search NEB's site directly.
• Cell Signaling Technology

Databases

Databases for specific fields or purposes. Also see "Information Resources" below for more general databases.

• REBASE (Restriction Enzyme Database): an extensive database of restriction endonuclease recognition sequences, isoschizomers, commercial availability and other useful information.
• PhosphoSite is a curated bioinformatics database developed by scientists at Cell Signaling Technology. Its goals are to aggregate information on all in vivo phosphorylation sites in human and mouse proteins and to provide information and resources that will facilitate signal transduction research.
• Phospho.ELM is a database of experimentally verified Serine, Threonine and Tyrosine sites in eukaryotic proteins, providing information about the phosphorylated proteins and the position of known phosphorylated instances, the kinases responsible and links to references. When available, additional information is given about structure, interaction partners and sub-cellular compartment and tissue specificities. The Phospho.ELM database can be searched using criteria such as protein name, kinase name or phospholigand binding domain.
• Complete Genome Tracking Database (COGENT) is a database of complete genomes and their protein sequences, where you can view the names of organisms, the site responsible for a sequence, the number of peptides and the genomic size; with links to the sites doing the sequencing work and FTP access to the peptide sequences.

Research Tools

Online tools and downloadable programs for molecular biology, some also including databases.

• Research Tools provides a host of links to research tools including databases, analysis tools, protocols, manuals, references - the list goes on.
• siRNA Target Finder is an siRNA design tool, on a secure web site to protect your sequence. You specify the length, GC% range, sequence region for siRNA target sites (or simply use the default setttings); the target mRNA nucleotide sequence by accession number, gene id, or pasted cDNA sequence; and the organism in which to conduct the RNA interference experiment. The design tool will find siRNA target sites based on your specifications and their strategies (and optionally, design RT-PCR primer sets at the same time). At the end, the candidate sequences will be filtered to remove non-unique sequences by BLAST against an unique and comprehensive EST/mRNA collection.
• RNA stuff @ tbi.univie.ac.at provides programs, web services, and databases, related to their work on RNA secondary structures, including the RNAfold service, which predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences up to 4000nt, consensus structure services, downloads and databases.
• Genomics and Bioinformatics Group at the USA's NIH provides many tools for data-mining biological information.
• Israel Science and Technology has numerous links to online software for sequence analysis, from searching the human genome, sequence alignment and primer design to protein secondary structure prediction.
• NEBCutter: online restriction digests and ORF analysis of DNA sequences up to 100 kb in length.
• Project Ensembl genome browser: easy access to sequences with a search engine plus structure prediction, identifying novel genes, and data mining functions.
• LabAssistant is a free downloadable program for Mac OSX that helps you organise your experiments, featuring multiple timers, reminders, and more. From Mek & Tosj.
• EnzymeX is a free downloadable program for Mac OSX to help you determine which restriction enzymes you should use to cut your DNA. Includes information on reaction conditions, suppliers, lab-specific information, and much more. From Mek & Tosj.
• DNA Artist is a collection of small molecular biology programs that are always up to date because it is an internet application. You can do things like search for Compatible Enzyme ends or do a PCR Melting point temperature calculation with different formulas, or you can run a Digest Preview of an Agarose Gel etc.
• PREDIKIN is a computer program that can be used to predict substrates for serine/threonine protein kinases.

Information Resources

• Bioprotocol: a site providing protocols for hundreds of protocols for molecular biology, arranged hierarchically, including both specific organisms or chemicals and topics such as DNA or RNA.
• Biovisa.net: Online protocol, journal and forum centre. Includes protocols for biology, biotech, biochemistry/molecular biology and other life sciences. Over a thousand protocols for biochemistry/molecular biology!
• Keoz6.com - Science Vertical Portal
• Directory of Open Access Journals: This service covers free, full text, quality controlled scientific and scholarly journals and aims to cover all subjects and languages. As of Dec 03 there were 672 journals in the directory.
• BIOSCI: a set of electronic communication forums - the bionet USENET newsgroups and parallel e-mail lists - used by biological scientists worldwide. No fees are charged for the service.
• PubMed: PubMed, a service of the US National Library of Medicine, provides access to over 11 million MEDLINE citations back to the mid-1960's and additional life science journals. PubMed includes links to many sites providing full text articles and other related resources.
• Scirus is a search engine site aiming to provide searches resulting in "scientific information only".

Distributed Computing Projects

Contribute your unused computer time to important life sciences research by making a distributed computing project your "screen saver". While you drink coffee, work at the bench or sleep, your computer can contribute its bits to scientific progress:

• Folding@Home is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases. As of April 2002, available for Mac OSX, Windows and Linux platforms. Join up and contribute to this important research.
• Grid.org is a single destination site for large-scale research projects powered by the United Devices grid computing solution, Grid MP Global. With the participation of over 2 million devices worldwide, grid.org projects like Cancer Research, Anthrax Research, and the new Smallpox Research Project have achieved record levels of processing speed and success.
• SETI@home is a scientific experiment that uses Internet-connected computers in the Search for Extraterrestrial Intelligence (SETI). You can participate by running a free program that downloads and analyzes radio telescope data for signals of artificial origin from outside our solar system. Available for Windows, Mac, Unix and more.