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

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/

Lab page: http://jarvislab.net/

The fellowship will be for a period of 3 years, or for a period of 4 years, with 25 % compulsory work (e.g. teaching responsibilities at the department) contingent on the qualifications of the candidate and the teaching needs of the department.

Starting date no later than October 1, 2021.

More at https://www.jobbnorge.no/en/available-jobs/job/199984/phd-research-fellow-in-genomics-and-bioinformatics

Basic Galaxy Tutorial

• RNA-Seq tutorial based on Trapnell et al. (2012) Nature Protocols

In this tutorial we cover the concepts of RNA-Seq differential gene expression (DGE) analysis using a very small synthetic dataset from a well studied organism.

Advanced Galaxy Tutorial

• RNA-Seq (Advanced) Tutorial

In this tutorial we compare the performance of three statistically-based differential expression tools:

* CuffDiff

* EdgeR

* DESeq2

Advanced Command Line Tutorial

• Graphical Output with CummeRbund introduces some basic commands using the cummeRbund package of the R programming language

You will need to install R, RStudio and cummeRbund on your PC (explained in the Tutorial). You will learn how to produce graphical output from RNA-Seq analysis previously done using a Cuffdiff analysis.

Variant Detection

Basic Galaxy Tutorial

• Variant Detection tutorial

In this tutorial we cover the concepts of detecting small variants (SNVs and indels) in human genomic DNA using a small set of reads from chromosome 22.

Advanced Galaxy Tutorial

• Variant Detection (Advanced) Tutorial

In this tutorial we compare the performance of three statistically-based variant detection tools:

* SAMtools: Mpileup

* GATK: Unified Genotyper

* FreeBayes

Each of these tools takes as its input a BAM file of aligned reads and generates a list of likely variants in VCF format

Pipelines are for those who are comfortable with using the UNIX command line; and often allow more control over branching and iteration logic.

• WGS/exome GATK-based variant calling pipeline

This is a basic variant-calling and annotation pipeline developed at the Victorian Life Sciences Computation Initiative (VLSCI), University of Melbourne. It is based around BWA, GATK and ENSEMBL and was originally designed for human (or similar) data. The master branch is configured for WGS data; there is an exome branch configured for variant calling in exome data.

To run the pipeline you will need Rubra: https://github.com/bjpop/rubra. Rubra uses the python Ruffus library: http://www.ruffus.org.uk/.

Protocols

• Familial Variant Calling

In this protocol we discuss and outline the process of calling familial related mutations.

• Somatic Variant Calling

In this protocol we discuss and outline the process of identifying somatic variants or mutations.

Assembly

Basic Galaxy Tutorial

• Genome assembly tutorial

In this tutorial we carry out de novo assembly of a microbial genome. We have also written a De novo Genome Assembly for Illumina Data Protocol for a more generic description of the method.

Protocol

• De novo Genome Assembly for Illumina Data

In this protocol we discuss and outline the process of de novo assembly for small to medium sized genomes. Use our Genome assembly tutorial to learn a specific case of using Galaxy to carry out de novo assembly of a microbial genome.

Small RNAs

Basic Galaxy Tutorial

• Quality control for small RNA

This tutorial covers initial steps of the workflow for analysis of short RNA expression such as a quality control of the raw reads, processing of the raw reads for the subsequent analysis and initial quality assessment of the library.

ChIP Seq

Protocol

• ChIP-Seq

In this protocol we discuss ChIP-Seq: a method to analyze the interaction between proteins and DNA.

Amplicons

Protocol

• Amplicon Alignment

In this protocol we discuss and outline the process of aligning custom amplicons using primers for high precision.

Learn Galaxy

Introduction to Galaxy, for those who are very new to Galaxy.

Using Histories and Workflows, for those with some Galaxy knowledge.

The Galaxy project website has many tutorials and screencasts about using Galaxy and the tools, and developing new tools.

Address of the bookmark: https://genome.edu.au/wiki/Learn

Applications are invited for the position of Senior Research Fellow for the following time-bound sponsored project as per the details given below:

1. BTIS project on, “Bioinformatics Center-National Infrastructural Facility in the Area of Immunology” funded by DBT

Senior Research Fellow (P) (One Position only)

Dr. Debasisa Mohanty
Staff Scientist-VI
deb@nii.res.in

Qualifications: M.Sc in Biological Sciences or Biotechnology with at least 04 years of Research experience in Bioinformatics or computational Biology after the master’s degree is essential.

Emoluments: The selected candidates will draw consolidated emoluments as per Institute Rules, depending upon qualifications & experience

Rs. 18,000/- per month consolidated plus 30% HRA if Leading to Ph.D/NET/GATE Qualified otherwise Rs. 14,000/- per month + 30% HRA.

Job description: The candidate should be well versed in programming in PERL/C++/HTML/CGI, web server and portal development, computational analysis of
protein structure & function, molecular dynamics simulations and use of high performance computing systems.

GENERAL TERMS AND CONDITIONS:-

1. The candidates selected for the above posts will be on contract for one year or duration of the project whichever is shorter, at a time.
2. No hostel/ housing facility will be provided.
3. Number of posts may vary and shall be need based. Advertisement is no commitment.
4. Applicants may clearly mention the category they belong to i.e. SC/ST/OBC/PH and attach documentary proof of the same.
5. No TA/DA will be paid for attending the interview, if called for.
6. Apart from sending application in the prescribed format given below, candidates should send complete Curriculum Vitae along with the names of three referees. Curriculum Vitae should contain details of the experimental expertise.

HOW TO APPLY Interested candidates may apply directly, STRICTLY IN THE PRESCRIBED FORMAT GIVEN BELOW, through e-mail, to the Investigator of the project, clearly indicating the name of the project along with their complete C.V., e-mail id, fax numbers, telephone numbers. Only Short listed candidates will be called for interview and they required to submit attested copies of all their certificates and a Demand Draft of Rs 100/- drawn on Canara Bank or Indian Bank payable at Delhi/New Delhi in favour of the Director, NII (SC / ST and PH candidates are exempted subject to submission of documentary proof), at the time of interview.

LAST DATE OF RECEIPT OF APPLICATIONS: 06th June, 2014

Advertisement

www1.nii.res.in/sites/default/files/projectappointment-Dr.Mohanty-6June2014.pdf

Address of the bookmark: https://github.com/schatzlab/appliedgenomics

The work will focus on the functional studies of small RNAs by using next-generation sequencing approaches.

Candidates should hold a Ph.D. degree and have strong background in bioinformatics.
The University of Nice Sophia-Antipolis provides a wide range of facilities and training essential for biomedical research.

Interested applicants should send a PDF with a cover letter stating research interests and qualifications, an updated CV, a summary of previous research experience and contact information for two references to Michele Trabucchi ( mtrabucchi@unice.fr )

Homepage: http://www.unice.fr/c3m/EN/Equipe10.html