Digital Tools & Resources

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

Databases

  • BioCyc
    • Collection of thousands of pathway/genome databases, plus software tools for understanding their data
  • BRENDA
    • Comprehensive enzyme information system
  • EcoGene
    • Database of all E. coli genes and sequences
  • Ecocyc
    • Comprehensive biochemical pathway and gene function site for E. coli
  • ENCODE
    • Parts list for functional elements in the human genome

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.

Protein

RNA

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

Research

Online tools

Tools available to use online.

General

  • Benchling
    • Online apps for cloning, molecular biology, and analysis
  • 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.
  • 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.
  • EMBL-EBI
    • Hugely extensive collection of resources, databases, and tools related to diverse aspects of bioinformatics and molecular biology
  • Inventory of Composable Elements (ICE) - 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.
  • iGEM Parts Registry
    • Formerly curated by MIT, this is an open repository of BioBricks; the place for all your standard biological parts.
  • NCBI
    • Various tools and databases for molecular biology.
  • 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.

DNA

  • BLAST
    • Finds regions of similarity between biological sequences.
  • 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.
  • GeneWarrior
    • Free/simple online toolset for sequence manipulation
  • 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.
  • 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
  • SIDD
    • Stress induced DNA duplex destabilization. Finds destabilized sites in superhelical DNA.
  • UNAFold
    • Replacement for mFold for predicting nucleic acid folding. Downloadable and some applications are available online also.

RNA

  • UNAfold by Michael Zuker.
    • Apps for predicting RNA and DNA folds, calculating Tm's and free energies. Runs mfold + UNAfold servers
  • Sfold: Statistical Folding and Rational Design of Nucleic Acids. Predicts accessible RNA sites
  • Vienna RNA software package: RNA secondary structure prediction and design

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.
  • 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.

Kits and Reagents

Statistical tests

Calculators

Office applications

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

Writing

  • Coredemia
    • Community for sharing and discussion of research papers
  • WriteBoard by 37signals
    • Permits writing of shareable, web-based text documents
  • Writely by Upstartle, LLC.
    • A beta word processor run over the web

Spreadsheets

  • 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.

General

  • CambridgeSoft
    • Numerous proprietary applications for research and composition (ChemBioDraw is usually accessible via academic institution email)
  • 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

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

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