Web resources

'''Please add new resources useful to the community here. Keep this page organized by following the format and organization already here.'''

 
 * See also Vectors for information and links related to cloning vectors.
 * See also Searching the literature for information and links on searching the biological literature.
 * See also Synthetic Biology for information and links on Synthetic Biology.

Videos

 * ScienceHack: Search engine for science videos with a review system for videos.

Information resources
References texts and information resources.

Bacterial physiology

 * Escherichia coli statistics by Institute for Biomolecular Design
 * Several tables describing statistical data on E. coli compiled from several sources.


 * Physiology of the Bacterial Cell by Neidhardt, Ingraham and Schaechter
 * Reference text on bacterial cell physiology.


 * EcoSal by ASM Press
 * An incomplete web version of the publication Escherichia coli and Salmonella: Cellular and Molecular Biology. [Subscription required]


 * EcoGene
 * Database of all E. coli genes and sequences


 * Ecocyc
 * Comprehensive biochemical pathway and gene function site for E. coli

Lab techniques

 * Current Protocols in Molecular Biology
 * Handbook of protocols.


 * Molecular Cloning by Sambrook and Russell
 * Handbook of protocols.


 * A Short Course in Bacterial Genetics by Miller
 * Handbook of protocols.


 * Polony Protocols by Church and Mitra Lab
 * Polonies are colonies of PCR amplicons derived from a single molecule of nucleic acid.


 * Gene expression in E. coli by Ehrmann lab
 * Tips and information on gene expression in E. coli


 * Protocol-online by Dr. Long-Cheng Li
 * A database of research protocols in a variety of life science fields. It has a popular discussion forum.


 * VADLO Search Engine
 * VADLO is the new search engine for Life Sciences Protocols, Online Tools, Databases, Software, and Biomedical Powerpoint Lectures. It also has Daily research cartoons, called *"Life in Research" Cartoons.

Protein

 * Technical suppport on protein crystallization by Hampton Research
 * Focused on protein crystallization but contains a lot of generally useful information about various reagents with respect to proteins.

RNA

 * Appendix by Ambion, Inc.
 * Website with many useful nucleic acid parameters.

Research

 * On Being a Scientist by National Academy of Science
 * NAS report on responsible conduct in research.

Online tools
Tools available to use online.

General

 * Colibri by Institut Pasteur
 * E. coli genome site; get sequences, see the position of your gene in the chromosome, see the function of your gene, and other fun stuff. You can also search for protein sequences/motifs within the E. coli genome.


 * NCBI
 * Various tools and databases for molecular biology.


 * Registry of Standard Biological Parts by MIT
 * Open repository of BioBricks; the place for all your standard biological parts.


 * The public instance of the JBEI Registry
 * A DNA part, plasmid, microbial strain, and Arabidopsis Seed online repository with physical sample tracking capabilities
 * A site where you can explore the various features of the JBEI Registry software, and even get some work done!
 * Try out the integrated online tools, including DNA sequence editing and annotation (Vector Editor) and auto-aligning sequencing trace files against a template.
 * Follow a link to the underlying open-source software source code.


 * Biopolymer calculator by Schepartz lab
 * Calculate extinction coefficients, Tm's, and base composition for your DNA or RNA; calculate amino acid composition and extinction coefficient for your protein
 * Currently under construction, with promises that it will be back online soon.


 * Bioinformatics Toolbox from DNA2.0
 * Contains many Javascript tools to do common tasks.


 * Science Gateway
 * Collection of science-related links, including links to journals, catalogs, and tools. See their about page.


 * BioNumbers
 * The database of useful biological numbers.


 * MetaBase
 * The database of biological databases

DNA

 * Clipboard by Austin Che
 * Web tool for getting complement, reverse complement, translation and restriction enzyme analysis of a DNA sequence


 * File format converter by Austin Che
 * Web tool for converting between sequence file formats.


 * Gene Design by Boeke lab
 * Collection of online tools for codon optimization and shuffling, restriction site editing, and so on.


 * NEB Cutter by New England Biolabs, Inc.
 * Tool for finding restriction sites, et cetera.


 * Primer3
 * Tool that lets you pick & evaluate primers from a DNA sequence


 * Search of rare codons in nucleotide sequence by "Practical Molecular Biology"
 * Rare Codon Calculator (RaCC) by NIH MBI Laboratory for Structural Genomics and Proteomics
 * Finds rare codons in a coding sequence.


 * UNAFold
 * Replacement for mFold for predicting nucleic acid folding. Downloadable and some applications are available online also.


 * SIDD
 * Stress induced DNA duplex destabilization. Finds destabilized sites in superhelical DNA.


 * j5 and DeviceEditor BioCAD online tools
 * j5: DNA assembly design automation for the SLIC/Gibson/CPEC and (combinatorial) Golden Gate assembly methods
 * DeviceEditor: a visual DNA design canvas that serves as front-end for j5

RNA

 * Promoter prediction: both prokaryote and eukaryotic promoter prediction


 * mFold by Michael Zuker.
 * This is the main page with links to sites for predicting RNA and DNA folds, calculating Tm's and free energies.
 * (This has been replaced with the DINAMelt server running UNAfold)
 * Vienna RNA software package: RNA secondary structure prediction and design
 * Sfold: Statistical Folding and Rational Design of Nucleic Acids. Predicts accessible RNA sites

Protein

 * AGADIR by Serrano lab
 * An algorithm to predict the helical content of peptides.


 * AVID by Keating lab
 * An integrative framework for discovering functional relationships among proteins.


 * Backbone-dependent rotamer library by Dunbrack lab
 * Libraries of sidechain rotamer from protein structures


 * Cn3D by NCBI
 * A helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.  It doesn't read PDB files but can be more straightforward to use than DeepView.


 * Contact Order Calulator by Baker lab
 * Calculator to determine a protein's contact order


 * ExPASy Proteomics server by the Swiss Institute of Bioinformatics
 * Collection of links to many pages to calculate parameters of your favorite proteins
 * Compute pI/Mw
 * A tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of Swiss-Prot and/or TrEMBL entries or for user entered sequences.
 * ProtParam
 * A tool which allows the computation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence.
 * Translate
 * Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.


 * GETAREA 1.1 by Sealy Center for Structural Biology
 * Solvent accessible surface areas, atomic solvation energies, and their gradients for macromolecules


 * PAIRCOIL2 by Keating and Berger labs
 * Tool to predict the parallel coiled coil fold from sequence using pairwise residue probabilities.


 * ProteinProspector by UCSF Mass Spectrometry Facility
 * Proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments.


 * Zinc Finger Tools by Barbas lab
 * Design Zinc Finger DNA binding proteins

Statistical tests

 * Statistics to use from Saint John's University.

Calculators

 * [GdmCl and [Urea] from refractive index] by Sosnick lab
 * GdmCl and urea concentration calculator from index of refraction.

Office applications

 * gOffice by Silveroffice, Inc.
 * Suite of office applications offered over the web


 * ThinkFree Office Online by ThinkFree
 * Beta suite of office applicatins offered over the web

Writing

 * Writely by Upstartle, LLC.
 * A beta word processor run over the web


 * WriteBoard by 37signals
 * Permits writing of shareable, web-based text documents


 * Google Documents by Google
 * Permits sharable, web-based word processor


 * Zoho Writer by Zoho
 * Permits sharable, web-based word processor

Spreadsheets

 * NumSum by TrimPath
 * Permits sharable, web-based spreadsheets


 * iRows by Itai Raz and Yoah Bar-David
 * Permits web-based spreadsheets


 * Zoho Sheets by Zoho
 * Permits sharable, web-based spreadsheets


 * Google Documents by Google
 * Permits sharable, web-based spreadsheets

Software resources
Software available to download.

General

 * Vector NTI by Informax, Inc.
 * Free-to-academics tool for sequence analysis and data management.

DNA

 * PerlPrimer: Open source PCR primer design. Written in Perl/Tk.
 * Artemis by the Sanger Center
 * A free DNA sequence viewer and annotation tool (Java based).


 * GeneDesigner by DNA2.0
 * Combine genetic building blocks by drag-and-drop, codon optimize, restriction site editing, sequence oligo design etc. See BMC Bioinformatics 2006 Jun 6;7(1):285 for more detail.
 * Free to download and works on Mac or PC. User agreement is somewhat restrictive, i.e. you cannot sell genes designed using the tool without permission.

RNA

 * XRNA: Java tools for creating RNA secondary structure diagrams

Protein

 * Dang by Richardsons' lab
 * A command-line tool that generates a table of several useful geometric measurements for each residue or base from a PDB file.


 * DeepView by GlaxoSmithKline & Swiss Institute of Bioinformatics
 * Awesome program for viewing and studying protein structure.


 * Modeller by Sali lab
 * Program for homology or comparative modeling of protein three-dimensional structures by satisfaction of spatial restraints.


 * PyMOL
 * Molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. The latest version does not run on OSX 10.3.  (from  Kathleen).


 * VMD by Theoretical and Computational Biophysics Group at UIUC
 * Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Generates pretty high resolution pictures of protein structures.

Geospatial modelling

 * GeoServer by The Open Planning Project
 * Although aimed at the geographic information systems community, the GeoTools toolkit from the GeoServer Project may be useful for geospatial problems in biology.

Gene Network Modeling

 * Ingeneue by George von Dassow, Eli Meir, Edwin Munro, and Garret Odell at the Center for Cell Dynamics
 * An open-source java program for modeling gene regulatory networks. Users can rapidly build networks by specifying their topology, initial conditions, connectivity, and known parameters.  Ingeneue can then search/explore paramter space for desired behavior, simulate the effects of noise and mutation, and generate statistics/time graphs of the system.

Toolbars

 * The Molecular Biologist's Toolbar by Bitesize Bio