An Autonomous National Institute under Government of India,
Ministry of Science & Technology
Department of Biotechnology

No: RGCB/ Advt./2014/1
January 24, 2014

Scientist Positions

Group Leader in Computational Biology/Bioinformatics
A highly motivated and innovative individual who will pursue basic research, solve biological problems with emphasis on computational and quantitative experimental methods and build active bridges to translational research. The scientist will also provide computational biology support to analyze complex data sets generated by RGCB scientists and collaborators.

Location: Thiruvananthapuram (Trivandrum)

The above positions will be at the E-II, F or equivalent levels. For senior applicants with an outstanding track record, an option of a contract career path for research excellence at Scientist G or H equivalent level can also be discussed. All positions will initially be for 5 years. Essential and desired qualifications as well as other relevant details for all the above positions are posted on the RGCB website (http://www.rgcb.res.in). The last date for receiving applications is March 14, 2014.

Sd/-
Director

Rajiv Gandhi Centre for Biotechnology
Thycaud, P.O., Poojappura,
Thiruvananthapuram, Kerala, India-695 014
Ph.: 91-471-2529400 (30 Lines), 2347975, 2348104, 2348753, 2345899
Fax: 91-471-2348096, 2346333

More at http://rgcb.res.in/jobs.html

The C-DAC will launch Param Bio Blaze, a supercomputing facility, to address the challenges in bioinformatics on Tuesday at a three-day symposium, titled: 'Accelerating biology: Computing life'. The supercomputing facility will be inaugurated on Tuesday by Ramakrishna Ramaswamy, vice-chancellor, Central University of Hyderabad at the Yashada. The new C-DAC's facility will have a capacity of 10 teraflop and will be able to analyse human cells and its functions.

Param Bio Blaze will help have a larger storage space and better computing facility for the bioinformatics sector. The facility will help capture the movement of molecules and also interaction between two molecules and the effects.

Applications of Param BioBlaze

- Collaboration with National Centre for Cell Science for research on Malaria and understanding how the disease spreads

- Collaborative work with Tata Memorial hospital on breast cancer and find out the difference between normal tissues and tissues from breast cancer patients

- Designing anti-cancer molecules, a collaborative research with the University of Pune

Reference:

Times of India

Image:datacenterjournal.com

However, the ancient invasions and migrations to slavery and trade, history is embroidered with events that led to interactions between previously separate populations. Early humans migrated due to many factors such as changing climate and landscape and inadequate food supply. Historical migration of human populations begins with the movement of Homo erectus out of Africa across Eurasia about a million years ago. Homo sapiens appear to have occupied all of Africa about 150,000 years ago, moved out of Africa 70,000 years ago, and had spread across Australia, Asia and Europe by 40,000 years BC. Indo-Aryan migration from the Indus Valley to the plain of the River Ganges in Northern India is presumed to have taken place in the Middle to Late Bronze Age, contemporary to the Late Harappan phase in India (ca. 1700 to 1300 BC). From 180 BC, a series of invasions from Central Asia followed, including those led by the Indo-Greeks, Indo-Scythians, Indo-Parthians and Kushans in the northwestern Indian subcontinent.

Using the recent advance technologies researchers have created a historical atlas of instances of such mixing. They use a sophisticated statistical method for making inferences about human history and infer populations interbredings ( happen over the past 4,000 years) with an ease.

The study published the findings and presented with an interactive map. http://admixturemap.paintmychromosomes.com/

These sort of genomic study have some limilation. It is hard to precisely define sources of mixing when it occurred between genetically similar groups, and scenarios involving multiple waves of mixing over time or between multiple groups can be difficult to tease apart. But it is believed that larger sample sizes will improve resolution. These high resolution will provide a deeper understanding of human history.

Reference:

http://www.sciencemag.org/content/early/2014/01/28/science.1245938

http://www.ncbi.nlm.nih.gov/pubmed/21390129?dopt=Abstract&holding=npg

http://www.csulb.edu/~kmacd/paper-ethnicity.html

Image: Wikipedia

Candidate Requirements: A PhD in computer science, computational biology, Bioinformatics, or a related field, along with sufficient programming skills for prototyping. Experience with next generation sequencing data analysis is required. Candidates with MS degree but with relevant work experience can also be considered. The successful candidate must be motivated and capable of working independently as well as in team environment.

Eligible and interested candidates can email your resumes to rohit at strandls dot com

About Strand Life Sciences: Strand was founded in 2000 by computer science and mathematics professors who recognized the need to automate and integrate life science data analysis through an algorithmic and computational approach. Strand’s solutions for life sciences research are robust and easy to use by the most novice user while powerful and configurable for the bioinformatician. Using its award-winning application development platform, AVADIS®, Strand builds innovative products that enable fast and cutting-edge analysis for basic and clinical research, drug discovery and development.

http://www.avadis-ngs.com/careers

Current computational interests:

Systematic analysis of genetic epistasis to identify redundant or compensatory systems and to reveal order of action in genetic pathways.
Using knockout, knockdown, or overexpression, or other perturbation experiments in combinations of genes in S. cerevisiae, C. elegans or mouse.
Using genome-scale genotyping of natural polymorphisms in S. cerevisiae and human populations.
Alternative splicing and its relationship to protein interaction networks.
Integrating large-scale studies including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns to quantitatively assign function to genes and guide experimentation.

More at http://llama.mshri.on.ca/index.html

Read more: https://edu.t-bio.info/amity-university-summer-bioinformatics-program-registrations-are-open/

1) Statistical machine learning methods for the analysis of medical
epigenomics data.

2) Sequence analysis algorithms for detection of RNA-DNA interactions.

Applicants should hold a M.Sc . or PhD in Computer Science or related
areas. Experience in the analysis of biological sequences, gene
expression and gene regulation is desirable. The candidate should have
solid programming skills (C, Python and/or R) and acquaintance with
Linux. Experience with high performance computing is a plus. The
working language of the group is English.

The position is based on the German TV-L 13 salary scale, including
all German social benefits (health insurance and pension scheme). The
expected starting date is September 2014. Interested candidates should
send a CV, statement of research interests and the names of three
references to jobs@costalab.org.

More at http://costalab.org/wp/phd-and-postdoc-position-in-computational-biology/

Seq is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host of domain-specific features and optimizations, Seq makes writing high-performance genomics software as easy as writing Python code, and achieves performance comparable to (and in many cases better than) C/C++.

Learn more by following the tutorial or from the cookbook.

Address of the bookmark: https://seq-lang.org

2. In some perl script I found this
 . . . . . .
 . . . . . .
# It works for me, only God understood how it is working
while (/(<\/[^>]+>)|(<[^>]+>)|(<[^>]+>)$|([^><]+)/go) {
            $startGene=$1;
            $beginChromosome=$2;
    
. . . . . .
 .. . . . . .
}

3. One more interesting message in Perl found …. It will must tickle you bone :)
open(my $fh, "<", "gene.txt")    or kill " Me if you think this is a mistake :$!";

4. From the Perl

  while () {  # "The Mothership Connection is here!"
    print “$_\n”; # Printing the offspring :)

5. Perl message
if ($1) { print “Just found a the error in chromosome !!!, yahoo…”; else { “That is not error, but mutation you moron!”;

6. One genome database curator walk in wine bar asked the bartender:
CREATE TABLE gene IF NOT EXISTS SexOnTheBeach;

Lab page: http://jarvislab.net/