• BigDataScript – A cross-system scripting language for working with big data pipelines in computer systems of different sizes and capabilities. [ paper-2014 | web ]
• Bpipe – A small language for defining pipeline stages and linking them together to make pipelines. [ web ]
• Common Workflow Language – a specification for describing analysis workflows and tools that are portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. [ web ]
• Cromwell – A Workflow Management System geared towards scientific workflows. [ web ]
• Galaxy – a popular open-source, web-based platform for data intensive biomedical research. Has several features, from data analysis to workflow management to visualization tools. [ paper-2018 | web ]
• Nextflow (recommended) – A fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. [ paper-2018 | web ]
• Ruffus – Computation Pipeline library for python widely used in science and bioinformatics. [ paper-2010 | web ]
• SeqWare – Hadoop Oozie-based workflow system focused on genomics data analysis in cloud environments. [ paper-2010 | web ]
• Snakemake – A workflow management system in Python that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment. [ paper-2018 | web ]
• Workflow Descriptor Language – Workflow standard developed by the Broad. [ web ]

SCHOOL OF COMPUTATIONAL AND INTEGRATIVE SCIENCES (SC&IS)

ESSENTIAL QUALIFICATION : - M.Sc./M.Tech. in Physics/ Chemistry/ Biology/ Mathematics/ Statistics/ Bioinformatics/ Computational Biology. Ph.D. in the broad areas of Bioinformatics/ Computational Biology. Candidates must have demonstrated capabilities in terms of high impact research publications in either of the above mentioned areas.

Scale of Pay : - 15600-39100/- (PB-III) AGP Rs. 6000/-

For more details on Centre/School, Specializations etc. please visit JNU website www.jnu.ac.in or contact Section Officer, Room Nos. 131-132, Recruitment Cell, Administrative Block, JNU, New Delhi – 110067, Email: recruitmentjnu2013@gmail.com The last date for the receipt of application is 15 May, 2014.

http://www.jnu.ac.in/Career/

http://www.jnu.ac.in/Career/ADVTNo_RC_48_2014.pdf
Last Apply Date:

15 May 2014

Address of the bookmark: https://github.com/broadinstitute/VariantBam

Computational methods used by the Shasta assembler include:

• Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads.
• Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10).

More at https://chanzuckerberg.github.io/shasta/index.html

Address of the bookmark: https://github.com/chanzuckerberg/shasta

WALK- IN –INTERVIEWS

Eligible candidates may appear in Walk-in-Interview on May 23, 2014 at 10 AM for the posts of Research Associates & Senior Research Fellows (SRF) in the following DST/DBT/ICAR funded projects.

1 NPTC Project on Bioinformatics and Comparative Genomics

Research Associate (One)

Rs. 24000/- + 30% HRA for masters degree holder with more than 4 years experience

Essential: Ph D in Plant Molecular Biology & Biotechnology/Genetics 0r Candidates who have already submitted their Ph D thesis in above subjects

Desirable: Research experience in Genomics, Molecular biology, Microarrays analysis, Gene cloning, transgenic Techniques , and computational analysis.

Senior Research Fellow ( UGCCSIR/ DBT/ ICAR Net qualified only): (One)

Rs. 16000/- + 30% HRA and Rs. 18000+30 HRA from 3rd year onwards

Essential:

1. ICAR/ UGCCSIR/DBT Net qualified only

2. M. Sc. (with thesis) in Biotechnology, Life Sciences, Biosciences/ Bioinformatics, Genetics/ Plant Pathology with experience in molecular biology.

Or M.Sc with more than 3 years research experiences

3. B.Sc. Agriculture or Biology

Desirable:
1. M. Sc. with thesis
2. Experience in molecular biology, plant tissue culture
3. Bioinformatics knowledge is important

2 DST JC Bose National Fellowship

Research Associate (Bioinformatics) : One

Rs.22000/- + 30% HRA for 1 & 2nd Yr., Rs. 23000+ 30% HRA for 3rd year and Rs. 24000+30% HRA for 4th &5th yr

Essential: M Ph D in Plant Molecular Biology & Biotechnology/Genetics

Desirable: Research experience in Genomics, Molecular biology, Microarrays analysis, Gene cloning, transgenic Techniques , and computational analysis.

Age limit: Max.35 years (Age relaxation of 5 years for SC/ST & women and 3 years for OBC)

The posts are purely temporary in nature and are co-terminus with the project. Initially the offer will be made for one year only and may be further extendable based on performance of the candidate. The interview will be held on May 23 , 2014 at 10:00 AM at NRCPB, LBS Building, Pusa Campus, IARI, New Delhi- 110012. The candidates must bring four copies of biodata (in the prescribed proforma), original certificates, attested photocopies of each of the certificates and an attested copy of recent passport size photograph. No. TA/DA would be given for the appearance in interview. Only the candidates having essential qualification would be entertained for the interviews. Short-listing of candidates based on academic merit and experience will be done in case of large number of applicants.

Advertisement: http://www.nrcpb.org/sites/default/files/Advertisement%20for%20RA%20and%20SRF%20Position.pdf

https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

Address of the bookmark: https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

C. Titus Brown http://video.open-bio.org/video/1/a-history-of-bioinformatics-in-the-year-2039

However, nanopore sequencing is an emerging and rapidly developing technology. It is not clear what will be most informative. We hope that IONiseR will provide a framework for visualisation of metrics that we haven’t thought of, and welcome feedback at mike.smith@embl.de.

If you’re not interested in the quality assement of the raw or event level data, and want to jump straight to the getting FASTQ format files from fast5 files you can go straight to the final section of this document.

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/IONiseR/inst/doc/IONiseR.html

The Indian scientists working in Bangalore, along with their American counterparts, have mapped more than 17,000 proteins in 30 organs of the human body. Just like the human genome was sequenced around the turn of the millennium, this is an equivalent mapping of the human proteome.

The researcher estimated there are around 20,500 proteins in the human body. These scientists have profiled around 17,294, which account for around 84% of the total proteins. Apart from this, the team also traced around 2,500 of 3,000 proteins that had been categorised as "missing proteins".

The work, done by group of Indian scientists, and Johns Hopkins University, published in the renowned journal Nature ( http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html ). Of the 72 people who worked on the project, 46 are Indians.

Reference:

http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html

http://www.proteinatlas.org/ -The antibody-based Human Protein Atlas programme

http://www.humanproteomemap.org/ -Proteogenomic analysis by identifying translated proteins from annotated pseudogenes, non-coding RNAs and untranslated regions.

https://www.proteomicsdb.org/ -Assembled protein evidence for 18,097 genes in ProteomicsDB