BioProgramming
The completion of the first human genome drafts was just a start of the modern DNA sequencing era which resulted in further invention, improved development toward new advanced strategies of high-throughput DNA sequencing, so called the “high-throughput next generation sequencing” (HT-NGS). The decreasing genome sequencing cost and desire to explore and understand biological machanism at genomic level, speed up the genomic sequencing projects. In the fast growing HT-NGS technologies, the main challenge is to cope with the analysis of vast production of sequencing database through advanced bioinformatics tools. In oder to develope sotware/tools bioinformatician/ biological programmers need to expertise in any one one the programming language. However, sometime one language are not enough to handle all sort of biological needs, which compel us to learn new biologically suitable language to handle ever growing genome or protein sequences.
The next step after reading genetic code is writing a script to analyse and explore the hidden information. This tutorial is aimed to introduce you new biological programming languages with their packages/libraries, and assist in your scripting work.
Navigate the sub-section of this page [ see right hand side of the page for it ]
Comments
Bioinformatics programming skills are becoming a necessity across many facets of biology and medicine, owed in part to the continuing explosion of biological data aggregation and the complexity and scale of questions now being addressed through modern bioinformatics. You can find out one paper explaining what are quickest way to learn bioinformatics programming languages.
A Quick Guide for Developing Effective Bioinformatics Programming Skills @
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2791169/
I found a news programming stuff for bioinformatician on internet, named BioBIKE, which can help and speed up biological programming. BioBIKE (biobike.csbc.vcu.edu) is a web-based environment enabling biologists with little programming expertise to combine tools, data, and knowledge in novel and possibly complex ways, as demanded by the biological problem at hand.
http://biobike.csbc.vcu.edu/
Research paper : http://nar.oxfordjournals.org/content/37/suppl_2/W28.full
BioJS is a library of graphical components easy to reuse to represent biological information. A library easy to maintain and develop by identifying minimal functional units that could be used as building blocks for more complex applications. A browser independent JavaScript library easy to integrate in web applications regardless the programming language used to develop the server side.
http://www.ebi.ac.uk/Tools/biojs/registry/
http://www.ebi.ac.uk/Tools/biojs/registry/components.html
http://biojs.github.io/biojs/
https://github.com/biojs/biojs
Biocoder: A programming language for standardizing and automating biology protocols. BioCoder, a C++ library that enables biologists to express the exact steps needed to execute a protocol. In addition to being suitable for automation, BioCoder converts the code into a readable, English-language description for use by biologists.
http://www.ncbi.nlm.nih.gov/pubmed/21059251
This microsoft new language can help to automate protocols http://research.microsoft.com/en-us/um/india/projects/biocoder/
http://www.jbioleng.org/content/4/1/13
A Quick Guide for Developing Effective Bioinformatics Programming Skills http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000589
Comparative study of biological programming language http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2267699/
tacg – a grep for DNA http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99049/