Digital Tools & Resources
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===Gene Network Modeling===
===Gene Network Modeling===
*[http://ingeneue.org Ingeneue] by George von Dassow, Eli Meir, Edwin Munro, and Garret Odell at [http://www.celldynamics.org
*[http://ingeneue.org Ingeneue] by George von Dassow, Eli Meir, Edwin Munro, and Garret Odell at [http://www.celldynamics.org 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.
Revision as of 23:55, 8 June 2006
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.
References texts and information resources.
- 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]
- 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.
- Appendix by Ambion, Inc.
- Website with many useful nucleic acid parameters.
- On Being a Scientist by National Academy of Science
- NAS report on responsible conduct in research.
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.
- 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.
- 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 DNA 2.0
- 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.
- Tool that lets you pick & evaluate primers from a DNA sequence
- Replacement for mFold for predicting nucleic acid folding. Downloadable and some applications are available online also.
- 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)
- 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
- 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.
- 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.
- 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
- Statistics to use from Saint John's University.
- [GdmCl] and [Urea] from refractive index by Sosnick lab
- GdmCl and urea concentration calculator from index of refraction.
- 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
- 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 available to download.
- Vector NTI by Informax, Inc.
- Free-to-academics tool for sequence analysis and data management.
- Artemis by the Sanger Center:
- A free DNA sequence viewer and annotation tool (Java based).
- 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 by
- a 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.
- 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.