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.
- ScienceHack: Search engine for science videos with a review system for videos.
References texts and information resources.
- 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]
- Database of all E. coli genes and sequences
- Comprehensive biochemical pathway and gene function site for E. coli
- 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.
- 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.
- Appendix by Ambion, Inc.
- Website with many useful nucleic acid parameters.
- On Being a Scientist by National Academy of Science
- NAS report on responsible conduct in research.
Tools available to use online.
- 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.
- 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.
- PaR-PaR Laboratory Automation Platform
- PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour.
- 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
- Science Gateway
- Collection of science-related links, including links to journals, catalogs, and tools. See their about page.
- The database of useful biological numbers.
- Clipboard by Austin Che
- Web tool for getting complement, reverse complement, translation and restriction enzyme analysis of a DNA sequence
- 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.
- 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.
- Replacement for mFold for predicting nucleic acid folding. Downloadable and some applications are available online also.
- Stress induced DNA duplex destabilization. Finds destabilized sites in superhelical DNA.
- j5, DeviceEditor, and VectorEditor online tools
- j5: DNA assembly design automation for (combinatorial) flanking homology (e.g., SLIC/Gibson/CPEC/SLiCE/yeast) and type IIs-mediated (e.g., Golden Gate/FX cloning) assembly methods
- DeviceEditor: a visual DNA design canvas that serves as front-end for j5
- VectorEditor: a visual DNA editing and annotation tool
- The j5 and DeviceEditor software has been exclusively licensed to TeselaGen Biotechnologies for commercial use and distribution.
- 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
- 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.
- 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 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
- Statistics to use from Saint John's University.
- [GdmCl] and [Urea] from refractive index by Sosnick lab
- GdmCl and urea concentration calculator from index of refraction.
- 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
- Writely by Upstartle, LLC.
- A beta word processor run over the web
- WriteBoard by 37signals
- Permits writing of shareable, web-based text documents
- NumSum by TrimPath
- Permits sharable, web-based spreadsheets
- iRows by Itai Raz and Yoah Bar-David
- Permits web-based spreadsheets
Software available to download.
- Vector NTI by Informax, Inc.
- Free-to-academics tool for sequence analysis and data management.
- 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.
- XRNA: Java tools for creating RNA secondary structure diagrams
- 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.
- 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.
- 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.