BOL: Related items

Important Journals, Blogs and Forums for Bioinformaticians

Jit — Wed, 08 Feb 2017 09:15:31 -0600

Journals. Most journals have RSS feeds for their current updates.

Blogs. Some of these blogs are very relevant to bioinfo jobs. Others are more personal interest.

The OpenHelix Blog
Ensembl blog
Galaxy News
Blue Collar Bioinformatics
Homologus
Golden Helix - our 2 SNPs
Genomics Law Report
R-bloggers (aggregates feeds from >350 blogs about R)
Genomes Unzipped
Jason Moore's Epistasis Blog
23andMe - the Spitoon

Variance Explained: David Robinson’s blog (Data Scientist at Stack Overflow, works in R and Python).
Global Biodefense: News on pathogens, outbreaks, and preparedness, with periodic posts on genomics and bioinformatics-related developments and funding opportunities.
In between lines of code: Lex Nederbragt’s blog on biology, sequencing, bioinformatics, …
Simply Statistics: A statistics blog by Rafa Irizarry, Roger Peng, and Jeff Leek.
Bits of DNA: Reviews and commentary on computational biology by Lior Pachter (fair warning: dialogue here can get a bit heated!).
Blue Collar Bioinformatics: articles related tool validation and the open source bioinformatics community.
Microbiome Digest – Bik’s Picks: A daily digest of scientific microbiome papers, by Elisabeth Bik, Science Editor at uBiome.
Living in an Ivory Basement: Titus Brown’s blog on metagenomics, open science, testing, reproducibility, and programming.
Enseqlopedia: James Hadfield’s blog on all things NGS.
Epistasis Blog: Jason Moore’s computational biology blog.
RStudio Blog: announcements about new RStudio functionality, updates about the tidyverse, and more.
nextgenseek.com: Next-Gen Sequencing Blog covering new developments in NGS data & analysis.
RNA-Seq Blog: Transcriptome Research & Industry News.
The Allium: We all need a little humor in our lives. Like The Onion, but for science.

Forums.

JRF Bioinformatics job vacancies in Tezpur University

Tue, 14 Feb 2017 16:40:26 -0600

Memo No. DoRD/CSE/SSS/20-295/112-A Date: 01/02/2017

Project Title : Integrating genome scale metabolic analysis of model plant pathogen Ralstonia solanacearum with RNAseq and fluxomics

Essential qualification : M.Tech. in CSE/IT (With specialization in Computational Biology/Bioinformatics) or M.Sc. in Bioinformatics/Biosciences/Molecular Biology Biotechnology preferably with NET/GATE/BET. Candidates should have minimum 55 % mark both in 10th and 10+2 Science examinations and mathematics at 10+2 Science. Desirable: Preference will be given to the candidates having experience in computational analysis of genome sequences or similar projects.

No. of Post : 01

Remuneration : Rs. 25,000/- for the 1st two years and Rs. 28,000/- for the 3rd year for SRF and applicable to the candidate having post graduate degree in Basic Science with NET/GATE/BET qualification or post graduate degree in professional course. Rs. 12,000/- for the 1st two years and Rs. 14,000/- for the 3 rd year for SRF,

Age : 28 years

Duration : Three (03) years or till completion of the project or until further order, whichever is earlier.

Hiring Process : Walk - In
Job Role: Research/JRF/SRF

Walk-in-interview will be held on 17th February, 2017, 11.15 a.m. at the office of the Head, Department of Computer Science and Engineering, Tezpur University.

Interested candidates may appear before the interview board with original documents from 10th standard onwards and photocopies of mark sheets, certificates, testimonials, caste certificate (if applicable), experience certificate certificates of NET/GATE/BET or similar examination qualifications, any other testimonials and a copy of recent curriculum vitae (CV) on the day of interview.

More at http://www.tezu.ernet.in/ProjectWalkin/Advt-DoRD-CSE-SSS-20-295-112-A.pdf

sockeye

Jit — Fri, 17 Feb 2017 08:51:16 -0600

This sockeye software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization.

Address of the bookmark: http://www.bcgsc.ca/platform/bioinfo/software/sockeye/releases/1.3

Postdoctoral Research Position in Bioinformatics in Milan

Thu, 20 Apr 2017 12:53:12 -0500

The lab of Immunobiology of Neurological Disorders has a main interest in the biological processes associated with multiple sclerosis, an inflammatory disorder of the central nervous system. The projects of interest for this application involve research on translational bioinformatics in complex human neurological disorders.

You have a PhD in Computational Science, Bioinformatics, or equivalent, and expertise in analysis and modeling of human RNA-seq data, statistics, data mining and machine learning. Excellent communication skills in English (written and oral) is a must. Flexibility and willingness to work across multiple projects and technologies in a rapidly evolving scientific context is required.
Salary will depend on qualification and experience. Starting date: immediate.

Interested candidates should send to farina.cinthia@hsr.it:

1. CV (please show evidences of relevant titles, projects, courses, references, etc.)
2. One page with a list of research topics (i.e. ongoing projects)
3. earliest availability

4. 2-3 contact names

Bioinformatics walk-in-interview at Tezpur University

Thu, 02 Mar 2017 04:24:46 -0600

A walk-in-interview will be held on 09 March, 2017, 11.15 a.m. at the office of the Head, Department of Computer Science and Engineering, Tezpur University for one (01) temporary position of Junior Research Fellow (JRF) in the DBT, Govt. of India sponsored project entitled “Integrating genome scale metabolic analysis of model plant pathogen Ralstonia solanacearum with RNAseq and fluxomics” under Dr. Siddhartha Sankar Satapathy (ssankar@tezu.ernet.in), Associate Professor, Department of Computer Science and Engineering, Tezpur University.

Interested candidates may appear before the interview board with original documents from 10th standard onwards and photocopies of mark sheets, certificates, testimonials, caste certificate (if applicable), experience certificate certificates of NET/GATE/BET or similar examination qualifications, any other testimonials and a copy of recent curriculum vitae (CV) on the day of interview.

Essential qualification: M.Tech. in CSE/IT (With specialization in Computational Biology/Bioinformatics) or M.Sc. in Bioinformatics/Biosciences/Molecular Biology Biotechnology preferably with NET/GATE/BET.

Candidates should have minimum 55 % mark both in 10th and 10+2 Science examinations and mathematics at 10+2 Science.

Desirable: Preference will be given to the candidates having experience in computational analysis of genome sequences or similar projects.

Remuneration: Rs. 25,000/- (Rupees twenty five thousand) only + HRA as admissible per month for the 1st two years and Rs. 28,000/- (Rupees twenty eight thousand) only + HRA as admissible per month for the 3rd year for SRF and applicable to the candidate having post graduate degree in Basic Science with NET/GATE/BET qualification or post graduate degree in professional course. Rs. 12,000/- (Rupees twelve thousand) only + HRA as admissible per month for the 1st two years and Rs. 14,000/- (Rupees fourteen thousand) only + HRA as admissible per month for the 3 rd year for SRF, for the candidate without NET/GATE/BET qualification. HRA will not be provided if campus accommodation is availed.

Age: Candidate shall not be more than 28 years of age on the date of interview. Upper age limit may be relaxed up to 5 years in the case of candidate belonging to SC/ST/ OBC/Women/Differently abled.

Duration: Three (03) years or till completion of the project or until further order, whichever is earlier.

N.B. No TA/DA will be paid to the candidates for attending the interview. For further details please contact: Dr. S. S. Satapathy Associate Professor Department of Computer Science and Engineering Tezpur University, Napaam-784028 Email: ssankar@tezu.ernet.in Contact no.: +91-9435979648

More Info: www.tezu.ernet.in/ProjectWalkin/Advt-DoRD-CSE-SSS-20-295-188-A.pdf

Fools guide

Poonam Mahapatra — Sun, 02 Apr 2017 14:31:18 -0500

This website and accompaning documents are intended as a tool to help researchers dealing with non-model organisms acquire and process transcriptomic high-throughput sequencing data without having to learn extensive bioinformatics skills. It covers all steps from tissue collection, sample preparation and computer setup, through addressing biological questions with gene expression and SNP data.

http://sfg.stanford.edu/denovo.html

http://sfg.stanford.edu/sequencing.html

http://sfg.stanford.edu/BLAST.html

http://sfg.stanford.edu/denovo.html

Address of the bookmark: http://sfg.stanford.edu/guide.html

ChromHMM: Chromatin state discovery and characterization

Abhimanyu Singh — Wed, 19 Apr 2017 04:06:23 -0500

ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks. ChromHMM is based on a multivariate Hidden Markov Model that explicitly models the presence or absence of each chromatin mark. The resulting model can then be used to systematically annotate a genome in one or more cell types. By automatically computing state enrichments for large-scale functional and annotation datasets ChromHMM facilitates the biological characterization of each state. ChromHMM also produces files with genome-wide maps of chromatin state annotations that can be directly visualized in a genome browser.

Address of the bookmark: http://compbio.mit.edu/ChromHMM/

Mapping NGS

Abhimanyu Singh — Tue, 02 May 2017 07:58:07 -0500

NGS data are just a bunch of sequences, you have no idea which region in the genome each sequences comes from, which gene it represents...
To know that you have to align the sequences to the reference sequence. The reference sequence is in most cases the full genome sequence but sometimes, a library of EST sequences is used.
In either way, aligning your sequence reads to the reference sequence is called mapping.

The most used mappers of DNA-seq data are BWA and Bowtie for DNA-Seq data and Tophat, STAR or HISAT for RNA-Seq data. Mappers differ in which options they can take in, how fast and how accurate they are. Bowtie is faster than BWA, but looses some sensitivity (does not map an equal amount of reads to the correct position in the genome).

Address of the bookmark: http://wiki.bits.vib.be/index.php/Mapping_of_NGS_data

Ten International Scholarships for Indian Biotechnology and Bioinformatics Students

Priya Singh — Wed, 10 May 2017 04:51:02 -0500

Wherever you go around the world, Indian students are in demand. With countries such as Canada and Australia providing huge incentives to Indian students to lure them to their shores, there are many institutions around the world that offer scholarships exclusively to Indian students. Historically these scholarships tend to be aimed towards Masters and PhD programmes however on the rise are scholarships for undergraduate students. Student World Online takes a look at ten international scholarships for Indian undergraduate students abroad.

1. TATA SCHOLARSHIP - Cornell University, New York State, USA
Tata, the Indian multinational conglomerate company, have a foundation known as the Tata Education & Development Trust which has endowed a multi million dollar sum to Cornell University to provide undergraduate scholarships to 20 Indian students every year. In another example of supporting American universities, the Tata group also pledged US$50 million to Harvard University in recent years, whose executive management programme Ratan Tata attended in the 1970s. Read more...

2. BRADMAN FOUNDATION SCHOLARSHIP - University of Wollongong, Australia.
Named after Australia's cricket legend Donald Bradman, the UOW Bradman Foundation Scholarship was launched in 2012, with the help of Adam Gilchrist no less, to offer one successful Indian student each year a 50% reduction in tuition fees. Read more...

3. HUAWEI MAITREE SCHOLARSHIPS - Various Universities, China
Along with Tata, Huawei are the other huge corporation to be featured. China's massive telecoms equipment vendor are involved in these scholarships offered to Indian students studying in China. In 2013 there are 10 generous scholarships available which provide full tuition fees and living expenses. The courses on which the scholarships are offered include Science and Technology courses, Social Sciences and Culture and Development courses. Read more...

4. DR. MANMOHAN SINGH SCHOLARSHIPS - Cambridge University, England, UK
These scholarships have been designed to help budding Indian minds follow in the footsteps of Indian prime minister Manmohan Singh by studying at the prestigious Cambridge University. The scholarships can be applied to any undergarduate course (with the two exceptions of medicine and veterinary science) and cover everything, i.e. tuition and college fees, living expenses and an additional grant to go towards travel expenses. Read more...

5. OXFORD AND CAMBRIDGE SOCIETY OF INDIA - Oxford & Cambridge Universities, England, UK
As the name might suggest, these are scholarships available for students wishing to study at Oxford or Cambridge (cleverly known together as Oxbridge). It is only available for applicants who are completing or have completed a degree at an Indian university, however these scholarships are for both undergraduate and graduate students. Read more...

6. EDINBURGH NAPIER UNIVERSITY - Scotland, UK
This one applies to all countries in the Indian subcontinent and is for both undergraduate and graduate courses. Edinburgh Napier University offers a merit based discount of £2,000 Pounds. Read more...

7. SHEFFIELD UNIVERSITY - Sheffield, UK
Provides merit-based scholarships for undergraduate and graduate programmes across all subjects. Read more...

8. INDIA 4EU II - Several Universities across Europe
Pioneered by the European Union and involving partner universities in France, Finland, Germany, Italy, Portugal, Spain and Sweden, the India 4EU II initiative is aimed at encouraging Indian students to study, work and live in Europe. The initiative is well funded and allows the successful students tuition fees, expenses for living and travel costs as well as insurance during their time at one of the partner universities. Read more...

9. TRINITY COLLEGE DUBLIN - Ireland
Valid for undergraduate courses in the faculties of Arts, Humanities, Social Sciences, Science, Computer Science or Engineering, the Trinity College Dublin offers Indian students scholarships to the tune of €9,000 per annum over a year degree course. Read more...

10. UNIVERSITY COLLEGE DUBLIN - Ireland
Another of Ireland and Dublin's finest, the UCD awards one Global Excellence Undergraduate Scholarship which provides the worthy student a substantial 50% towards their tuition fees and is valid for all courses save medicine, radiography and veterinary medicine. UCD also offers a Global Undergraduate Scholarship scheme for undergrads accepted on science, social sciences, arts and business courses. This is all thanks to a €250,000 fund that will allow for 57 Indian students to benefit from scholarships at UCD. Read more...

CABOG: Celera Assembler with Best Overlap Graph

Abhimanyu Singh — Mon, 15 May 2017 05:04:39 -0500

CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as mammalian. CABOG is an extension of the Celera Assembler software that was originally developed at Celera for the 2001 publication of the first draft human genome sequence. The software was released to the public domain in 2004. Its open source repository on Source Forge is an internet resource for scientists around the world.

CABOG is one of many software programs called genome assemblers. These programs exist to overcome the fundamental limitation of all sequencing machines, namely, that they read out very few DNA letters at a time. These programs reconstruct genomes that are billions of letters long from the hundreds of letters per read that modern sequencers provide. What these programs do is often described as a scaled up version of a family solving a jigsaw puzzle.

The CABOG software was the first to accomplish many scientific goals. It was the first to assemble the genome of a multicellular organism (Drosophila melanogaster, 2000). It was the first to assemble both parental haplotypes of one human genome (J. Craig Venter, 2007). It was the first to assemble environmental sequence from the oceans (Sargasso Sea in 2004 and Global Ocean Sampling in 2007). It was first to combine reads from first-generation Sanger sequencing machines and second-generation pyrosequencing machines (Marine microbes, 2006). Today, CABOG is one of the leading assembly programs for data sets that include paired end data from the Roche 454 line of sequencing machines.

Address of the bookmark: http://www.jcvi.org/cms/research/projects/cabog/overview/