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Saturday, 1 August 2015

How database virtualisation helped the EBI save datacentre space

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The European Bioinformatics Institute recently scooped the award for Best Datacentre Project at the CW European User Awards, and here's why In its role as data custodian, it’s up to the European Bioinformatics Institute (EBI) in Cambridge to ensure the world’s biological information is freely available and accessible for use by the global scientific community.

  • The non-profit is currently sitting on 50,000TB of biological data, which is distributed across three UK datacentres. Scientists from academia and the commercial world are invited to use these datacentres for research, app development or staff training purposes.
  • According to EBI calculations, it fields around 12 million requests each month for access to this data worldwide.
  • Users can choose to download and analyse it locally or use EBI’s own infrastructure as a service (IaaS) to do the deed and – in turn – save themselves the hassle of finding somewhere to store it all on-premise.

“This is a fairly new approach and is feeding into the different ways the life science community wants to consume and deliver research. We’re seeing prototypes of this model coming out in a range of life science areas,” says Steven Newhouse, head of technical services at EBI.

  • With around 20% of the EBI’s 570 staff devoting their time to carrying out collaborative and investigation-led life science research, the amount of data the organisation has to manage is doubling every year.
  • At the current rate of generation, the data the organisation manages is expected to grow over the next five years to around 1.5 million TB, putting huge pressure on EBI’s data infrastructure and operations.

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Friday, 31 July 2015

Bioinformatics Strategy Meeting Europe 2015

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Bioinformatics Strategy Meeting Europe 2015

Bioinformatics - Research Officer

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The Garvan Institute of Medical Research is one of Australia’s leading medical research institutes, with over 600 scientists, students and support staff.  We pioneer study into the most widespread diseases affecting our community today, including cancer, neurodegenerative and mental diseases, disorders of the immune system, diabetes and obesity, osteoporosis and other skeletal disorders.
The Ovarian Cancer Research Laboratory at the Garvan Institute has a particular interest in the application of genomic technologies to address clinically significant issues such as primary and acquired chemoresistance. The lab spans the Garvan Institute and the Peter MacCallum Cancer Centre (Melbourne) through Professor David Bowtell’s joint appointment at these two leading institutions.

Garvan Institute of Medical Research

  • The Bioinformatics Research Officer will focus on the implementation, development and support of computational and statistical tools for the analysis and interpretation of next-generation sequencing (NGS) data. Specifically, the Bioinformatics Research Officer will assist and provide insights into the genomic analysis of primary and acquired chemoresistance in ovarian cancer. In addition to providing support for the existing team, the Bioinformatics Research Officer will have the opportunity to develop their own research interests, as we expand on our previous work describing whole genome sequencing (WGS) of chemoresistant ovarian cancer (Patch et al. 2015 Nature).

Responsibilities will include:

  • Establish and optimise a bioinformatics pipeline for the analysis of NGS data
  • Variant verification and expression analysis using transcriptome data
  • Analysis of SNP array data to determine copy number and explore phylogenetic relationships between tumour samples
  • Integrative analyses combining WGS, copy number, methylation and expression data
  • Statistical analyses, such as associating molecular features with clinical outcomes
  • Keeping abreast of advances in genomic technologies and informatics tools

Qualifications, skills and experience required:

  • PhD in Bioinformatics or equivalent experience in a related field
  • Excellent computational background, especially in the management of large data sets in unix/linux environment
  • High proficiency in programming and scripting languages (e.g. C/C++, Java, Perl, Python)
  • Advanced user of the R programming language and R-based statistical packages and tools, such as those available from the Bioconductor project for high throughput genomic data analysis
  • Good knowledge of statistics and presentation of molecular/clinical data
  • Experience in the analysis and interpretation of large genomic data sets (WGS, RNAseq)
  • A proven track record, e.g. publications, grants, software/tool development

The Offer

  • Garvan offers a friendly and professional work environment in state of the art modern building and facilities, on-site café, social club and close to cafes and public transport. You’ll be rewarded with a competitive salary, above market Superannuation and attractive salary packaging options. This role is Full-time for an initial 2 year fixed term contract.

How to apply

Please prepare your application and submit via the directions below:

  • Cover Letter addressing the Selection Criteria above
  • Your CV including 3 Referees
  • Relevant Academic Transcripts / qualifications

Closing date

  • This role will remain open until filled. We are reviewing applications as we receive them.

Apply Online

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Thursday, 30 July 2015

Bioinformatics Jobs in India

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Research Associate under Network Project on Agricultural Bioinformatics

ICAR -Central Institute for Research on Buffaloes, Hisar (Haryana) will conduct walk-in-interview for contractual positions of Research Associate (One) and Senior Research Fellow (Two) as per detail mentioned below.

Name of the project Network Project on Agricultural Bioinformatics
Number of positions One
Qualifications Ph.D Degree in Bioinformatics/Biotechnology/ Biochemistry/ Genetics & Breeding/Life Sciences OR Master’s Degree in relevant subject with at least 2 years research experience. Desirable: Working experience in Molecular Biology/ Genomics/Bioinformatics, specifically, sequence data analysis using software’s proficiently.
Emoluments Master’s Degree Holders Rs. 38,000/- per month Doctoral Degree Holders Rs. 40,000/- per month
Date and time of reporting for Interview 11.08.2015 at 11.00 AM. at ICAR-CIRB, Hisar (Haryana)

Senior Research Fellow (SRF) under AICRP on Nutritional and Physiological Interventions for Enhancing Reproductive Performance in Animals”

Name of the project

“AICRP on Nutritional and Physiological Interventions for Enhancing Reproductive Performance in Animals”

Qualifications Master’s Degree in Animal Reproduction, Animal Nutrition, Animal Physiology or Life Sciences. Desirable: Ph.D in relevant field/experience of working in a research project
Emoluments Rs.25000/- per month for 1st and 2nd year and Rs. 28000/- per month for 3rd year.
Date and time of reporting for Interview 11.08.2015 at 11.00 AM. at ICAR-CIRB, Hisar (Haryana)

Senior Research Fellow (SRF) under National Agricultural Scientific Fund (NASF) project on “Lactation stress associated postpartum anestrus SNP array in buffaloes”

Name of the project National Agricultural Scientific Fund (NASF) project on “Lactation stress associated postpartum anestrus SNP array in buffaloes”
Qualifications Master’s Degree in Vety. Reproduction, Animal Physiology, Animal Biotechnology or Life Sciences. Desirable: Ph.D in relevant field/experience of working in related field.
Emoluments Rs.25000/- per month for 1st and 2nd year and Rs. 28000/- per month for 3rd year
Date and time of reporting for Interview 11.08.2015 at 11.00 AM. at ICAR-CIRB, Hisar (Haryana)

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Project Fellow @ Central University of Himachal Pradesh

Applications on plain paper giving complete permanent and correspondence address including telephone no. and email address (if available), details of educational qualifications (starting from High School or equivalent) and/or experience if any along with attested copies of all mark sheets/ certificates are invited for the post of Project Fellow in the ongoing SERB-DST sponsored research project under the Young Scientist scheme entitled “Genome-wide screening of Outer Membrane Proteins in Mycobacterium avium subsp. paratuberculosis(MAP) K-10: a repertoire of candidate immunogens for translational medicine”(Project No. SB/YS/LS-125/2014)on the following terms and conditions:

Terms and conditions/Important Instructions

  • Post Name:Project Fellow
  • Post:one
  • Salary:Rs.14000/-+ 10% HRA per month
  • Duration:Initially for one year (extendible for two more years). The post will be co-terminus with the project
  • Educational Qualification: Master Degree with minimum 55% marks in any branch of Life Sciences/Chemistry/Computer Science/Pharmacy.
  • Desirable Qualification: Experience in basic Bioinformatics and Molecular Biologytechniques

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Project Fellow @ CSIR-National Chemical Laboratory

Applications are invited in the prescribed Proforma for filling up of position of Project Fellow on a purely temporary basis. The detail of the Sponsored Project under which engagement is proposed to be made is as under:

How to Apply:

  • The application in the prescribed Proforma (enclosed here with) duly completed and signed together with photo-copies of relevant certificates/testimonials & photograph should be addressed to: The Head, Biochemical Sciences Division (Attn to

Dr. Narendra Kadoo), CSIRNational Chemical Laboratory, Pune 411008, & submitted so as to reach the office on or before 11/08/2015

  • The prescribed educational qualifications are a bare minimum and merely possessing of same will not entitle candidates to be called for interview. Where number of applications received in response to this Notice of engagement is large, it may not be convenient or possible to interview all the candidates. Based on the recommendation of the Screening Committee, the Project Leader may restrict the number of candidates to be called for interview to reasonable limits after taking into consideration qualifications and experience over and above the minimum qualifications prescribed in the Notice. Therefore, it will be in the interest of the candidates, to mention all the qualifications and experience in the relevant field at the time of applying.
  • The candidates recommended by the Screening Committee to be called for written test / interview would be notified on the Divisional Notice Board on 14/08/2015. The candidates may ascertain the information by contacting on the telephone nos.: 020- 25902238 / 2647, or by email to ny.kadoo@ncl.res.in /ya.waichal@ncl.res.in.

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Research Fellows @ The Wildlife Institute of India (WII)

The Wildlife Institute of India (WII) is a premier national autonomous Institute of the Ministry of Environment, Forest & Climate Change, Government of India, in the field of teaching, training and research. The WII wishes to engage 11 research personnel viz., 02–Project Biologists, 01–Research Associate, 01–Senior Research Fellow, 01–Project Assistant, 01–Project Fellow and 05–Junior Research Fellows (Indian national only) through a walk-in-interview on Monday, 24th August 2015. The details of the available positions along with essential and desirable qualifications, terms and conditions and how to apply are given below:

Project Title, details of position and duration

  • Population Genetic Structure of Nilgiri Tahr (Hemitragus hylocrius) in Western Ghats, India: Conservation and Forensic Implications. (01 – Research Associate) Duration: Three years

Essential Qualification

  • Ph.D. in Life Science (Biotechnology/Animal Genetics/Conservation Genetics/Molecular Biology) from a recognized University.

Desirable Qualification

  • Knowledge and experience in bioinformatics and working experience in conservation genetics.

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Wednesday, 29 July 2015

The Increasing Speed of Bioinformatics

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The speed of implementation for genetic engineering is faster than ever. As a result, implications are larger and the stakes are higher.

BIOGRAPHY OF Raymond McCauley:

Raymond McCauley is a scientist, engineer, and entrepreneur working at the forefront of biotechnology. Raymond explores how applying technology to life — biology, genetics, medicine, agriculture — is affecting every one of us.. He is known for using storytelling and down-to-earth examples to show how quickly these changes are happening, right now.Read More


Friday, 17 July 2015

Creating ‘genomic origami’

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In a triumph for cell biology, researchers have assembled the first high-resolution, 3-D maps of entire folded genomes and found a structural basis for gene regulation, a kind of “genomic origami” that allows the same genome to produce different types of cells. The research appears online Thursday in the journal Cell.
  • A central goal of the five-year project, a collaboration among researchers at Harvard University, Baylor College of Medicine, Rice University, and the Broad Institute of Harvard and MIT, was to identify the loops in the human genome. Loops form when two bits of DNA that are far apart in the genome sequence end up in close contact in the folded version of the genome in a cell’s nucleus.
  • Researchers used a technology called “in situ Hi-C” to collect billions of snippets of DNA that were later analyzed for signs of loops. The team found that loops and other genome folding patterns are an essential part of genetic regulation.

A 3D Map of the Human Genome

“More and more, we’re realizing that folding is regulation,” said study co-first author Suhas Rao, a researcher at Baylor’s Center for Genome Architecture and a 2012 graduate of Harvard College. “When you see genes turn on or off, what lies behind that is a change in folding. It’s a different way of thinking about how cells work.”

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Oldest Neanderthal DNA found in Italian skeleton

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The calcite-encrusted skeleton of an ancient human, still embedded in rock deep inside a cave in Italy, has yielded the oldest Neanderthal DNA ever found.

These molecules, which could be up to 170,000 years old, could one day help yield the most complete picture yet of help paint a more complete picture of Neanderthal life, researchers say.

  • Although modern humans are the only remaining human lineage, many others once lived on Earth. The closest extinct relatives of modern humans were the Neanderthals, who lived in Europe and Asia until they went extinct about 40,000 years ago. Recent findings revealed that Neanderthals interbred with ancestors of today's Europeans when modern humans began spreading out of Africa — 1.5 to 2.1 percent of the DNA of anyone living outside Africa today is Neanderthal in origin. [Image Gallery: Our Closest Human Ancestor]
  • In 1993, scientists found an extraordinarily intact skeleton of an ancient human amidst the stalactites and stalagmites of the limestone cave of Lamalunga, near Altamura in southern Italy — a discovery they said had the potential to reveal new clues about Neanderthals.

"The Altamura man represents the most complete skeleton of a single nonmodern human ever found," study co-author Fabio Di Vincenzo, a paleoanthropologist at Sapienza University of Rome, told Live Science. "Almost all the bony elements are preserved and undamaged."

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