Related Research Articles
Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The subsequent process of analyzing and interpreting data is often referred to as computational biology, though the distinction between the two terms is often disputed.
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has foundations in applied mathematics, chemistry, and genetics. It differs from biological computing, a subfield of computer science and engineering which uses bioengineering to build computers.
The Open Bioinformatics Foundation is a non-profit, volunteer-run organization focused on supporting open source programming in bioinformatics. The mission of the foundation is to support the development of open source toolkits for bioinformatics, organise developer-centric hackathon events and generally assist in the development and promotion of open source software development in the life sciences. The foundation also organises and runs the annual Bioinformatics Open Source Conference, a satellite meeting of the Intelligent Systems for Molecular Biology conference. The foundation participates in the Google Summer of Code, acting as an umbrella organisation for individual bioinformatics-related projects.
Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan, Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge.
RasMol is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data Bank (PDB).
PyMOL is a source-available molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. As the original software license was a permissive licence, they were able to remove it; new versions are no longer released under the Python license, but under a custom license, and some of the source code is no longer released. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. According to the original author, by 2009, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.
Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology.
Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in chemistry and biochemistry.
The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics. It is available for Windows, Linux, Unix, and macOS. It is free and open-source software distributed under the GNU Lesser General Public License (LGPL) 2.0.
The Common Lisp Interface Manager (CLIM) is a Common Lisp-based programming interface for creating user interfaces, i.e., graphical user interfaces (GUIs). It provides an application programming interface (API) to user interface facilities for the programming language Lisp. It is a fully object-oriented programming user interface management system, using the Common Lisp Object System (CLOS) and is based on the mechanism of stream input and output. There are also facilities for output device independence. It is descended from the GUI system Dynamic Windows of Symbolics' Lisp machines between 1988 and 1993.
... you can check out Common Lisp Interface Manager (CLIM). A descendant of the Symbolics Lisp machines GUI framework, CLIM is powerful but complex. Although many commercial Common Lisp implementations actually support it, it doesn't seem to have seen a lot of use. But in the past couple years, an open-source implementation of CLIM, McCLIM – now hosted at Common-Lisp.net – has been picking up steam lately, so we may be on the verge of a CLIM renaissance. – From Practical Common Lisp
BALL is a C++ class framework and set of algorithms and data structures for molecular modelling and computational structural bioinformatics, a Python interface to this library, and a graphical user interface to BALL, the molecule viewer BALLView.
Physiomics is a systematic study of physiome in biology. Physiomics employs bioinformatics to construct networks of physiological features that are associated with genes, proteins and their networks. A few of the methods for determining individual relationships between the DNA sequence and physiological function include metabolic pathway engineering and RNAi analysis. The relationships derived from methods such as these are organized and processed computationally to form distinct networks. Computer models use these experimentally determined networks to develop further predictions of gene function.
Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It is extensible via a plugin architecture.
geWorkbench is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the programming language Java. geWorkbench uses a component architecture. As of 2016, there are more than 70 plug-ins available, providing for the visualization and analysis of gene expression, sequence, and structure data.
Pharmaceutical bioinformatics is a research field related to bioinformatics but with the focus on studying biological and chemical processes in the pharmaceutical area; to understand how xenobiotics interact with the human body and the drug discovery process.
References
- ↑ Biopython License
- ↑ "GeWorkbench License". geWorkbench. Columbia University. 15 June 2014.