Digital Tools & Resources

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How to use this page

Please help us by adding new digital resources useful to the community here. Keep this page organized by following the
format and alphabetical organization already in place.

All of the links below are organized first by whether they are general reference or a more specified research tool.
The sub-categories are organized alphabetically by research topic. Note that many of the tools listed may fit into
multiple categories, but are only listed once. Tools of this type may be tagged with other relevant categories by
adding a link to another section of the page after the description. Use the *link format of the following DNA example:

QIIME (Quantitative Insights Into Microbial Ecology) software
Powerful suite of open source bioinformatics tools for performing microbiome analysis from raw sequences. *RNA

This allows for quick navigation around the page and the use of the * in Ctrl + F searches to differentiate between
sections and page body content.

Please help keep this page up to date by fixing old or broken links and by deleting listings that no longer work. If
you think that an item has been placed in the wrong category, feel free to move it. Please be cautious when downloading
software, and make sure to help the community by removing links with harmful content. Content with questionable scientific
value should also be removed.

All information resources are assumed to be online, but research tools should be tagged with web for online resources, software
for downloadable items, and app for items used on phones and tablets. Please tag any additional categories in this
way if needed. Additional suggestions for format changes may be executed directly or discussed on the talk page.

Information resources

References, texts, and information resources.


Search engines and data repositories. There are thousands available (see MetaBase). The few items listed here are some of the broadest and most powerful

General Search/Reference

    • Hugely extensive collection of resources, databases, and tools related to diverse aspects of bioinformatics and molecular biology, often containing everything one might need

Genome and Metabolism

  • BioCyc
    • Collection of thousands of pathway/genome databases for many organisms, plus software tools for understanding their data
  • Colibri by Institut Pasteur
    • E. coli genome browser; 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.
  • EcoGene
    • Database of all E. coli genes and sequences (Entrez data is pulled from here)
  • EcoCyc
    • Comprehensive biochemical pathway and gene function site for E. coli
    • Parts list for functional elements in the human genome
  • 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.
  • KEGG
    • Genomic database geared towards high-level functions of the biological system
  • MetaCyc
    • Multi-organismal member of BioCyc collection; catalogs entire universe of metabolism
  • SGD
    • Saccharomyces genome database (yeast genome)


    • Comprehensive enzyme information system
  • ConSurf
    • Server for the identification of functional regions in proteins
  • Genome3D
    • Consensus structural annotations and 3D models for sequences of model organisms (built upon numerous other useful related resources)
  • UniProt
    • Extensive database of protein sequence and functional information


  • Appendix by Ambion, Inc.
    • Website with many useful nucleic acid parameters.
  • GreenGenes
    • 16S rRNA database and workbench (most recently updated data can be downloaded here)
  • Ribosomal Database Project
    • Quality-controlled, aligned and annotated Bacterial and Archaeal 16S rRNA sequences, and Fungal 28S rRNA sequences, and a suite of analysis tools
    • Massive, searchable rRNA database (especially strong for microbes)


  • Addgene's Vector DB
    • Addgene is a a non-profit plasmid repository where scientists can archive and share their plasmids. Addgene assists with data submission and all tech transfer issues. Plasmids can be requested from Addgene for a fee to cover expenses.
    • AddGene Vectors can be directly imported into Genome Compiler software platform, in which you can easily edit and visualize it.

Lab Techniques

  • Barrick Lab of UT Austin
    • Tons of helpful resources like protocols, guides, links, and tools for lab work
  • BenchFly
    • Search, view, upload, create, and host scientific protocol videos
  • OWW Materials
    • Useful information for making or obtaining reagents, enzymes, buffers, etc.
  • OWW Protocols
    • Growing collection of laboratory protocols and 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.
  • app web
    • Huge, open access life science protocol repository for discovery and sharing of scientific methods

Microbial physiology

  • CyberCell Database (CCDB) 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)
  • MicrobeWiki
    • Student edited resource on microbes and microbiology (curated pages reviewed by microbiologists)


  • PhET
    • Interactive simulations for science and math
  • ScienceHack
    • Search engine for science videos with a review system

Research Tools

Tools and applications to aid in research tasks.


  • Benchling web
    • Online apps for cloning, molecular biology, and analysis
  • Genome Compiler web software
    • A powerful, free online & downloadable genetic engineering all-in-one platform for molecular & synthetic biologists
  • FastPCR software
    • An integrated tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching
  • Galaxy web
    • Easy-to-use Bioinformatics manipulation tools for UCSC data
  • iGEM Parts Registry web
    • Formerly curated by MIT, this is an open repository of BioBricks; the place for all your standard biological parts.
  • Ingeneue by George von Dassow, Eli Meir, Edwin Munro, and Garret Odell at the Center for Cell Dynamics software
    • 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.
  • MABL web
    • Reconstruct and analyze phylogenetic relationships between molecular sequences
  • OpenCFU software
    • Local cell colony counting software
  • MCDS software
    • All-in-one molecular cloning and genetic engineering design, simulation & management tool for complex synthetic biology and metabolic engineering project.
  • PaR-PaR Laboratory Automation Platform web
    • 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.
  • Pinecone by Serotiny web
    • High-level design, analysis and transmission of protein constructs. Pinecone matches users' designs with CRO's or DNA synthesizers to produce genetic starting material (dsDNA, plasmid or purified protein). Facilitates mutation and combinatorial protein sets that benefit from manufacturing economies of scale.
  • PubChase software app
    • Generates research article recommendations unique to each user. Site also has a special academic community.
  • Science Gateway web
    • Collection of science-related links, including links to journals, catalogs, and tools. See their about page.


  • OligoCalc Oligonucleotide Calculator web
    • Calculate a number of parameters for your nucleotide polymers


  • Artemis by the Sanger Center software
    • A free DNA sequence viewer and annotation tool (Java based). The Sanger Center also develops a number of other miscellaneous tools for download
  • BioEdit software
    • Windows-only sequence alignment editor (no longer maintained, but free to download)
  • BLAST web
    • Finds regions of similarity between biological sequences.
  • CLC Sequence Viewer software
    • Software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, graphical viewing, and output options.
  • Gene Design by Boeke lab web
    • Collection of online tools for codon optimization and shuffling, restriction site editing, and so on.
  • GeneDesigner by DNA2.0 software
    • 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.
  • GeneWarrior web
    • Free/simple online toolset for sequence manipulation
  • Genome Compiler web software
    • The Complete set of tools for sequence viewing, annotation and alignment. Free online & downloadable and supports all file formats
  • IDT SciTools web
    • A number of web tools and calculators to assist in the design and execution of molecular biology research
  • Jalview software
    • Program for multiple sequence alignment editing, visualization, and analysis
  • NEB Cutter by New England Biolabs, Inc. web
    • Tool for finding restriction sites, et cetera.
  • PerlPrimer software
    • Open source PCR primer design. Written in Perl/Tk.
  • Primer3 web
    • Tool that lets you pick & evaluate primers from a DNA sequence
  • QIIME (Quantitative Insights Into Microbial Ecology) software
    • Powerful suite of open source bioinformatics tools for performing microbiome analysis from raw sequences.
  • SIDD web
    • Stress induced DNA duplex destabilization. Finds destabilized sites in superhelical DNA.
  • UNAFold web
    • Replacement for mFold for predicting nucleic acid folding. Downloadable and some applications are available online also.
  • USEARCH software
    • High throughput sequence analysis (orders of magnitude faster than BLAST) and other software tools


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


  • AGADIR by Serrano lab web
    • An algorithm to predict the helical content of peptides.
  • AVID by Keating lab web
    • An integrative framework for discovering functional relationships among proteins.
  • Cn3D by NCBI web
    • 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.
  • Dang by Richardsons' lab software
    • 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 software
    • Awesome program for viewing and studying protein structure.
  • ExPASy Proteomics server by the Swiss Institute of Bioinformatics web
    • 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 by Sealy Center for Structural Biology web
    • Solvent accessible surface areas, atomic solvation energies, and their gradients for macromolecules
  • Metazome web
    • Proteome-level phylogeny and genomics
  • Modeller by Sali lab software
    • Program for homology or comparative modeling of protein three-dimensional structures by satisfaction of spatial restraints.
  • PAIRCOIL2 by Keating and Berger labs web
    • Tool to predict the parallel coiled coil fold from sequence using pairwise residue probabilities.
  • ProteinProspector by UCSF Mass Spectrometry Facility web
    • Proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments.
  • PyMOL software
    • 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 software
    • 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.


  • ApE A plasmid Editor software
    • Simple tools for plasmid design and manipulation
  • GeneDesigner by DNA 2.0 software
    • Design genes de novo with a powerful and intuitive user interface
  • Genome Compiler web software
    • A free all-in-one platform for intuitive vector design and automatic assembly. Supports main construction techniques, manual and auto sequence annotation, alignment, primer design and compatible to all file formats.
  • j5, DeviceEditor, and VectorEditor web
    • 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
  • PlasMapper web
    • Generates and annotates a plasmid map based on sequence data
  • Serial Cloner software
    • Light and intuitive tools for diverse molecular biology manipulations
  • SnapGene Viewer software
    • Free version of SnapGene. Allows mapping of DNA up to 1 Gb in length. Convenient viewing and annotation tools for genetic constructs.
  • Vector NTI software
    • Powerful but expensive vector editor. Supports most sequence types and easily manipulates genetic constructs.


  • CambridgeSoft software
    • Numerous proprietary applications for research and composition (ChemBioDraw is usually accessible via academic institution email)
  • Coredemia web
    • Community for sharing and discussion of research papers
  • Evernote software app
    • Powerful cross-platform note-taking, composition, and organization with cloud syncing.
  • InstaGrok software
    • Tool for seeking, collecting, and mapping information
  • Inkscape web
    • Free, feature-rich drawing program with support for SVG and PDF images
  • Mendeley software app
    • Powerful and straightforward local and cloud-based reference manager
  • Origin software
    • Scientific graphing and data analysis software
  • Qiqqa software
    • Organize, annotate, search, and cite references from a PDF library (loads of extra features)
  • ReadCube software
    • Reference manager, similar to Mendeley or Evernote. Can enhance PDFs and search PubMed from within the app.
  • Vessel web app
    • Digital lab notebook for organizing and sharing experiments, findings, protocols, and more.
  • WriteBoard by 37signals web
    • Permits writing of shareable, web-based text documents
  • Writely by Upstartle, LLC. web
    • A beta word processor run over the web
  • Zoho web
    • Sharable, web-based word processing, spreadsheets, and presentations (alternative to Google Docs)

See also:

Vectors - info/links related to cloning vectors.

Searching the literature - info/links on searching the scientific literature.

Synthetic Biology - info/links on Synthetic Biology.