EDUCATIONAL RESOURCES

UMUC: Bioinformatics Studies
The Master of Science program in biotechnology serves a number of careers at the entry-, mid-, or high-level positions, depending on the prior level of experience of the candidate.
A specialization in Bioformatics covers a broad range of subjects (for example, biostatistics, databases and data structures, algorithms, gene expression analysis, and PERL) at the interface of molecular biology and computational science. [read more]

A guide to bioinformatics resources on the internet
The following list contains link to various bioinformatics related resources available on the internet. This list is by no means exhaustive, but does cover a large bulk of the bioinformatics material and subject matters. [read more]

Online Lectures on Bioinformatics
In the current context we can only give an extremely brief introduction to the basic notions of molecular biology. An overview can be found in any modern textbook on biology, biochemistry or molecular biology [read more]

Centre for Molecular and Biomolecular Informatics
The C MB I offers a number of Courses on Bioinformatics and Cheminformatics topics, which are described elsewhere, as well as a number of Interactive Web Tutorials.
These online tutorials are available for anyone to browse, but we know from years of experience teaching computational biology and chemistry courses at the CMBI that doing carefully designed exercises with an experienced instructor close at hand is the best way to learn. [read more]

What is Bioinformatics?

Bioinformatics is the application of computer technology to the management of biological information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied to scientific research, gene-based drug discovery and development. The need for bioinformatics capabilities has been precipitated by the explosion of publicly available genomic information resulting from the Human Genome Project. The goal of this project – determination of the sequence of the entire human genome (approximately three billion base pairs) was reached in 2003. The science of bioinformatics, which is the melding of molecular biology with computer science, is essential to the use of genomic information in understanding biological evolution, human diseases, and in the identification of new molecular targets for drug discovery. In recognition of this, many universities, government institutions and pharmaceutical firms have formed bioinformatics groups, consisting of computational biologists and bioinformatics computer scientists. Such groups will be key to unraveling the mass of information generated by large scale sequencing efforts underway in laboratories around the world.

bioplanet.com

What are the most common Bioinformatics programs?

Everyday bioinformatics is done with sequence search programs like BLAST, sequence analysis programs, like the EMBOSS and Staden packages, structure prediction programs like THREADER or PHD or molecular imaging/modelling programs like RasMol and WHAT IF.

More:

  • NetSurfP - Protein Surface Accessibility and Secondary Structure Predictions
  • NetTurnP - Prediction of Beta-turn regions in protein sequences
  • MODELLER - Used for homology or comparative modeling of protein three-dimensional structures
  • AutoDock - Suite of Automated Docking Tools
  • Gromacs - A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids

bioinformatics.org

What are the most common Bioinformatics technologies?

Currently, a lot of bioinformatics work is concerned with the technology of databases. These databases include both "public" repositories of gene data like GenBank or the Protein DataBank (the PDB), and private databases, like those used by research groups involved in gene mapping projects or those held by biotech companies. Making such databases accessible via open standards is very important. Consumers of bioinformatics data use a range of computer platforms: from the more powerful and forbidding UNIX boxes favoured by the developers and curators to the far friendlier Macs often found populating the labs of computer-wary biologists.

Databases of existing sequencing data can be used to identify homologues of new molecules that have been amplified and sequenced in the lab. The property of sharing a common ancestor, homology, can be a very powerful indicator in bioinformatics.

bioinformatics.org

How is data analyzed in Bioinformatics?

Bioinformatics tools can be used to obtain sequences of genes or proteins of interest, either from material obtained, labeled, prepared and examined in electric fields by individual researchers/groups or from repositories of sequences from previously investigated material.

Both types of sequence can then be analyzed in many ways with bioinformatics tools.

They can be assembled. Note that this is one of the occasions when the meaning of a biological term differs markedly from a computational one (see the amusing confusion over the issue at Web-based geek forum Slashdot). Computer scientists, banish from your mind any thought of assembly language. Sequencing can only be performed for relatively short stretches of a biomolecule and finished sequences are therefore prepared by arranging overlapping "reads" of monomers (single beads on a molecular chain) into a single continuous passage of "code". This is the bioinformatic sense of assembly.

They can be mapped***---that is, their sequences can be parsed to find sites where so-called "restriction enzymes" will cut them.

They can be compared, usually by aligning corresponding segments and looking for matching and mismatching letters in their sequences. Genes or proteins that are sufficiently similar are likely to be related and are therefore said to be "homologous" to each other---the whole truth is rather more complicated than this. Such cousins are called "homologs".

If a homolog (a related molecule) exists, then a newly discovered protein may be modeled---that is the three dimensional structure of the gene product can be predicted without doing laboratory experiments.

Bioinformatics is used in primer design. Primers are short sequences needed to make many copies of (amplify) a piece of DNA as used in PCR (the Polymerase Chain Reaction).

Bioinformatics is used to attempt to predict the function of actual gene products.

Information about the similarity, and, by implication, the relatedness of proteins is used to trace the "family trees" of different molecules through evolutionary time.

There are various other applications of computer analysis to sequence data, but, with so much raw data being generated by the Human Genome Project and other initiative in biology, computers are presently essential for many biologists just to manage their day-to-day results

Molecular modelling / structural biology is a growing field which can be considered part of bioinformatics. There are, for example, tools which allow you (often via the Net) to make pretty good predictions of the secondary structure of proteins arising from a given amino acid sequence, often based on known "solved" structures and other sequenced molecules acquired by structural biologists.

Structural biologists use "bioinformatics" to handle the vast and complex data from X-ray crystallography, nuclear magnetic resonance (NMR) and electron microscopy investigations and create the 3-D models of molecules that seem to be everywhere in the media.

bioinformatics.org

How is BioINFO Project involved with Bioinformatics?

BioINFO Project, a division of Pangaea Biosciences, was created as a free, open source platform for students, educators, and researchers. At Pangaea Biosciences, we value the importance of scientific excellence. We strongly believe the field(s) of biotechnology:bioinformatics present a number of vital opportunities. By employing the latest scientific applications toward medicine and biology, Pangaea Biosciences seeks to help improve techniques for medical treatments & diagnostics, personal & homeland security, environmental monitoring & ecosystem restoration, water & food safety, evolutionary studies and much more. We are dedicated to upholding our commitment to serving you, our community, and the integrity of our profession.

The main initiative of BioINFO Project is to provide a wide array of integrative tools & applications to better equip private corporations and academic institutions toward scientific advancement.



The BioINFO Project

"Merging science & technology to create innovative solutions."