[BojanaL]

Open source databases in biology, chemistry, bioinformatics….

I can’t agree more about importance of open sourcing in biotechnology. Lack of money prevents lot of scientist and laboratories around the world from conducting experiments that could potentially improve human life either through faster drug development, or safer and more successful food production. Shared data could accelerate R&D by saving time and resources.

Here are examples of currently used open source databases:

Open source databases used in cheminformatics:

*Chemistry Development Kit (CDK)

This database is open source library for chemoinformatics and bioinformatics. It was developed at the University of Notre Dame in 2000. So far, 75 people contributed to the project. As from 2012, CDK is supported by InChI Trust (promotes and improves the International Chemical Identifier standard).

Main features:

• 3D geometry generation
• substructure search using exact structures and SMARTS-like queries
• QSAR descriptor calculation
• fingerprint calculation
• protein active site detection
• cognate ligand detection
• metabolite identification
• pathway databases

*JOELib

JOELib software is mainly used for conversion of chemical file formats. All Java supporting systems could use JOELib.

Main features:

• Query and substructure search
• Clique Detection
• QSAR
• Feature/descriptor calculation
• Fingerprint calculation
• Chemical file formats

Open source databases used in microscope image processing:

*CellProfiler

CellProfiler is free software designed to read and analyze microscopically obtained images (obtained through fluorescent microscopy, for example). When object of interest is identified, it could be further analyzed in more details.

*ImageJ

ImageJ is developed by National Institute of Health. It’s Java based program designed for image processing. It’s used in 3D live-cell imaging and radiological imaging to edit, process and analyze obtained images. Also, ImageJ can be used for comparison of multiple imaging… It supports number of formats: TIFF, PNG, GIF, JPEG, BMP, FITS...

Open source databases used in molecular dynamics:

*Ascalaph Designer

Ascalaph Designer is software developed for molecular modeling and simulation. Some of the features are associated with molecular dynamics and quantum chemistry. It’s mainly applied in modeling and building of polymers like nano-tubes, proteins, nucleic acids, lipid bilayers….

*GROMACS

GROMACS (GROningen MAchine for Chemical Simulations) is developed at the University of Groningen to be used in simulation of proteins, lipids and nucleic acids. It’s one of the fastest and most popular software in molecular dynamics field.

Open source databases used for viewing of molecules:

*Jmol

Jmol is Java based molecular viewer for 3D chemical structures. “Applets” is popular feature of Jmol that allows displaying molecules in a variety of ways: "ball and stick" models, "space filling" models, "ribbon" models…It supports a wide range of molecular file formats including pdb, cif, mol, CML....

*PyMOL

PyMOL is molecular visualization system designed by Warren Lyford DeLano who wanted to incorporate open source practice in medical field as much as possible. This tool is used in molecular modeling and can produce high quality 3D images of various molecules. PyMOL is applicable in structural biology associated research. It’s free of charge for scientific and educational communities.

Open source databases used in biology:

*Systems Biology Ontology (SBO)

Systems Biology Ontology is set of terms commonly used in systems biology, especially in computational modeling. It’s part of the BioModels.net that define standards for model curation, vocabularies for annotating models and provide publicly accessible database of annotated, computational models in SBML and other structured formats. SBO is designed by Computational Neurobiology Group (UK) and the SBML Team (USA); it’s funded by European Molecular Biology Laboratory and the National Institute of General Medical Sciences.

*UGENE

Ugene is open source bioinformatics software with integrated (well known) biological tools and algorithms.

Main features:

• Creating, editing and annotating nucleic acid and protein sequences
• Multiple sequence alignment: Clustal, MUSCLE, Kalign, MAFFT, T-Coffee
• Restriction analysis with integrated REBASE restriction enzyme database
• Integrated Primer3 package for PCR primers design
• Search for direct, inverted and tandem repeats in DNA sequences
• Search for transcription factor binding sites with weight matrix and SITECON algorithms
• Search for ORFs
• Cloning in silico
• Protein secondary structure prediction with GOR IV and PSIPRED algorithms
• Building and viewing phylogenetic trees
• Local sequence alignment with optimized Smith-Waterman algorithm
• Visualization of next generation sequencing data using UGENE Assembly Browser

Number of open source databases is large and I hope that their number will increase even more in the future.