Digital Tools & Resources

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

• See also:
  • Vectors - info/links related to cloning vectors.
  • Searching the literature - info/links on searching the biological literature.
  • Synthetic Biology - info/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

Search engines and data repositories

Genome and Metabolism

• BioCyc
  • Collection of thousands of pathway/genome databases, plus software tools for understanding their data

• 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

• Ensembl
  • Eukaryotic genome browser

• Ensembl Genome
  • Sister to Ensembl, not limited to Eukaryotes

• 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

• Mammalian Gene Collection
  • Access to sequence-validated, full-length, protein-coding, mammalian cDNA clones

• MetaCyc
  • Multi-organismal member of BioCyc collection; catalogs entire universe of metabolism

• SGD
  • Saccharomyces genome database (yeast genome)

• UCSC Genome Bioinformatics
  • Sequence reference for a large number of genomes

Protein

• BRENDA
  • Comprehensive enzyme information system

• Genome3D
  • Consensus structural annotations and 3D models for sequences of model organisms (built upon numerous other useful related resources)

• 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.

• UniProt
  • Extensive database of protein sequence and functional information

RNA

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

• SILVA
  • Massive, searchable rRNA database (especially strong for microbes)

General Search/Reference

• CDC Disease Conditions
  • Filtered index of diseases from the CDC database

• EMBL-EBI
  • Hugely extensive collection of resources, databases, and tools related to diverse aspects of bioinformatics and molecular biology

• Entrez (NCBI)
  • Search all NCBI databases

• MetaBase
  • The database of biological databases - External link

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

• Tree of Life
  • Collaborative encyclopedia of biodiversity

Lab techniques

• Current Protocols in Molecular Biology
  • Handbook of protocols. (Links to Wiley Online Library)

• Gene expression in E. coli by Ehrmann lab
  • Tips and information on gene expression in E. coli

• Molecular Cloning by Sambrook and Russell
  • Handbook of protocols. Subscription only. External link

• 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.

• 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.

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

• Benchling
  • Online apps for cloning, molecular biology, and analysis

• Bioinformatics Toolbox from DNA2.0
  • Contains many Javascript tools to do common tasks.

• BioNumbers
  • The database of useful biological numbers. (link to database)

• 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.

• Cancer Genome Anatomy Project
  • Resources and tools related to the characterization of cancer gene expression profiles

• 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.

• Experiment
  • Crowdfunded scientific research

• Galaxy
  • Easy-to-use Bioinformatics manipulation tools for UCSC data

• iGEM Parts Registry
  • Formerly curated by MIT, this is an open repository of BioBricks; the place for all your standard biological parts.

• MABL
  • Reconstruct and analyze phylogenetic relationships between molecular sequences

• 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.

• PhET
  • Interactive simulations for science and math (fun, teaching)

• Science Gateway
  • Collection of science-related links, including links to journals, catalogs, and tools. See their about page.

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

• 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.

• 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

• Rare Codon Calculator (RaCC) by NIH MBI Laboratory for Structural Genomics and Proteomics
  • Finds rare codons in a coding sequence.

• Search of rare codons in nucleotide sequence by "Practical Molecular Biology"

• 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

• Promoter prediction: both prokaryote and eukaryotic promoter prediction

• 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.

• 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.

Composition 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

• Coredemia
  • Community for sharing and discussion of research papers

• Google Documents by Google
  • Permits sharable, web-based word processor

• WriteBoard by 37signals
  • Permits writing of shareable, web-based text documents

• Writely by Upstartle, LLC.
  • A beta word processor run over the web

• 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

• 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.

• Mendeley
  • Powerful and straightforward local and cloud-based reference manager

• OpenCFU
  • Local cell colony counting software

• Qiqqa
  • Organize, annotate, search, and cite references from a PDF library (loads of extra features)

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.

• Jalview
  • Program for multiple sequence alignment editing, visualization, and analysis

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

• USEARCH
  • High throughput sequence analysis (orders of magnitude faster than BLAST) and other software tools

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