Difference between revisions of "Digital Tools & Resources"

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**Currently under [http://www.schepartzlab.yale.edu/construction.html construction], with promises that it will be back online soon.
**Currently under [http://www.schepartzlab.yale.edu/construction.html construction], with promises that it will be back online soon.
*[https://www.dna20.com/index.php?pageID=216] from DNA2.0
*[https://www.dna20.com/index.php?pageID=216 Bioinformatics Toolbox] from DNA2.0
**Contains many Javascript tools to do common tasks.
**Contains many Javascript tools to do common tasks.

Revision as of 07:34, 17 September 2009

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.

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.
  • 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

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



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


Online tools

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.
  • NCBI
    • Various tools and databases for molecular biology.
  • 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.
  • BioNumbers
    • 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.
  • Primer3
    • Tool that lets you pick & evaluate primers from a DNA 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.


  • 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.
  • 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.
  • 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.

Statistical tests


Office applications

  • gOffice by Silveroffice, Inc.
    • Suite of office applications 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 resources

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.


  • 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.
  • 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

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.