Digital Tools & 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 [1]

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 (combinatorial) SLIC/Gibson/CPEC and 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
  1. 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.
  2. 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.
  3. 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