BOL: Related items

Pimp your brain: Bioinformatics

Wed, 20 Aug 2014 22:09:21 -0500

Jan Lisec from the Max Planck Institute of Molecular Plant Physiology explains, in this "pimp your brain" episode, what bioinformatics is and why bioinformatics is so important and indispensable for biological research. In the video serial "Pimp your brain" scientists from the Max Planck Institute of Molecular Plant Physiology describe their research. More videos from the 'Pimp your brain' serial are available on www.youtube.com/playlist?list=PL-l9VItC9Gn2Ur2Xj6PTOAkjLUlVPbIOO More videos are available on www.mpimp-golm.mpg.de

GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments

Shruti Paniwala — Mon, 11 Jun 2018 05:43:44 -0500

GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap closure. We demonstrate with sequencing data from various organisms that the gap-closing accuracy of GMcloser is 3–100-fold higher than those of other available tools, with similar efficiency. https://academic.oup.com/bioinformatics/article/31/23/3733/209212

Address of the bookmark: https://academic.oup.com/bioinformatics/article/31/23/3733/209212

Center for Molecular Dynamics Nepal (CMDN), Nepal

Wed, 23 Jul 2014 13:54:51 -0500

Center for Molecular Dynamics Nepal (CMDN), established 2007 prides itself as a research driven nongovernmental organization. Unlike other civil society organizations, CMDN is dedicated entirely to promoting research in the country. With its team of energetic and highly motivated experts, CMDN is now recognized as the leading public health and wildlife research organization of the country.

More at http://www.cmdn.org.np/main/index.php

You can't hide from Genome Hackers

Neel — Sat, 13 Oct 2018 14:17:28 -0500

Young computational biologist named Yaniv Erlich shocked the research world by showing it was possible to unmask the identities of people listed in anonymous genetic databases using only an Internet connection

Paper: http://science.sciencemag.org/content/early/2018/10/10/science.aau4832

More at https://www.wired.com/story/genome-hackers-show-no-ones-dna-is-anonymous-anymore/

Senior Research Fellow at NIT, Rourkela

Wed, 30 Jul 2014 00:53:13 -0500

NATIONAL INSTITUTE OF TECHNOLOGY, ROURKELA – 769 008(ORISSA)
SPONSORED RESEARCH, INDUSTRIAL CONSULTANCY & CONTINUING EDUCATION

ADVERTISEMENT NO: NITR/SR/CH-BIF/2014/30

Applications are invited on prescribed format for the following assignment in a purely time bound research project undertaken in the Department of Biotechnology & Medical Engineering of the Institute.

1. Name of the Temporary Post : Senior Research Fellow-01
2. Name of the Research Project: “ Bioinformatics Infrastructure Facility (BIF)”
3. Name of the Sponsoring Agency: DBT, Government of India, 4 Tenure of the Project : 12th Five year Plan
5 Tenure of the Assignment : 01 year [Likely to be extended for 04 more years]
6 Job Description : BIF Maintenance and Active Research in Bioinformatics
7. Consolidated monthly compensation / Fellowship: Rs.18,000/- P.M.

8. Essential Qualifications and experience: B.Tech with valid GATE Score or M.Tech degree in Biotechnology/Bioinformatics/Computer Science/Computational Biology
9. Desirable Qualifications/ Experiences: Experience of Programming in PERL,R, Python, Unix and Visual Studio + Knowledge in NGS data analysis work flows ,WGS and statistical packages such as CRAN-R,MATLAB etc.

10. Accommodation : Bachelor accommodation in the Institute may be provided subject to availability.
11. For technical information on the project, the candidate may contact the Principal Investigator at the following address:

Name : Prof. Mukesh K Gupta
Address : Dept. of Biotechnology & Medical Engineering,
N.I.T.Rourkela-769 008
Telephone No : 0661-2462294
E-mail : guptam@nitrkl.ac.in

Eligible persons may apply in the prescribed format (available in the Institute Website)affixed with coloured photographs to be submitted in duplicate along with photo copies of relevant certificates, grade/ mark sheets, publications etc., to Asst. Registrar, SRICCE,
National Institute of Technology, Rourkela–769 008 before 22.08.2014. The cover should be super- scribed clearly the post applied for & Name of the Project.

Mere possession of minimum qualification does not guarantee invitation to the interview.
Candidates will be short listed based on merit and need of the project.

http://www.nitrkl.ac.in/IntraWeb/Jobs_Tenders/Jobs/ProjectFellowship/2014/141707192838_1.pdf

pWhatsHap: a parallel, high-performance version of WhatsHap

Jit — Wed, 14 Nov 2018 08:20:27 -0600

Given the potential relevance of efficient haplotyping in several analysis pipelines, we have designed and engineered pWhatsHap, a parallel, high-performance version of WhatsHap. pWhatsHap is embedded in a toolkit developed in Python and supports genomics datasets in standard file formats. Building on WhatsHap, pWhatsHap exhibits the same complexity exploring a number of possible solutions which is exponential in the coverage of the dataset. The parallel implementation on multi-core architectures allows for a relevant reduction of the execution time for haplotyping, while the provided results enjoy the same high accuracy as that provided by WhatsHap, which increases with coverage.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1170-y

Address of the bookmark: https://bitbucket.org/whatshap/whatshap

Studentship and Traineeship in Bioinformatics at Barkatullah University, Bhopal

Thu, 07 Aug 2014 16:57:00 -0500

Department of Biotechnology & Bioinformatics Center
Barkatullah University, Bhopal – 462 026

Studentship and Traineeship in Bioinformatics

Applications are invited on plain paper from suitable candidates for Studentship and Traineeship (One each) at Bioinformatics Sub-Center as detailed below:

1. Studentship: Studentship is for those who have completed M. Sc. Degrees in Life Science.

Number of seats : One

Duration : Six months

Eligibility : Passed M.Sc. degree in Life Sciences.

Fellowship : Rs. 5000/- (Five thousand only) per month

2. Traineeship: Traineeship is for those who have completed M. Sc. Degrees in Life Science/Registered Ph. D. student in Life Sciences.

Number of seats : One

Duration : Six months

Eligibility : Passed M.Sc. degree in Life Sciences/ Registered Ph. D. student in Life Sciences

Fellowship : Rs. 5000/- (Five thousand only) per month

Preferences will be given to person who has experience in Bioinformatics and Computer
sciences. The application along with detailed bio-data should reach the undersigned, on or before 25th August 2014. Both, the studentship and the traineeship are temporary, will be discontinued after the six months from the date of Joining. It may be discontinued in-between without any notice, if the work is not found satisfactory.

Advertisement www.bioinfobubpl.nic.in/Advertisement_st.pdf

Genome Annotation using MAKER tutorial !

Shruti Paniwala — Thu, 20 Dec 2018 17:39:23 -0600

MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.

Address of the bookmark: https://www.biostars.org/p/261203/

Genome assembly forensics: finding the elusive mis-assembly

Jit — Sat, 26 Jan 2019 18:02:01 -0600

We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline, called amosvalidate. We demonstrate the application of our pipeline in both bacterial and eukaryotic genome assemblies, and highlight several assembly errors in both draft and finished genomes. The software described is compatible with common assembly formats and is released, open-source, at http://amos.sourceforge.net.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2397507/

http://amos.sourceforge.net/wiki/index.php/AMOS

Address of the bookmark: http://amos.sourceforge.net/wiki/index.php/AMOS

Guest Faculty at Pondicherry University

Wed, 20 Aug 2014 00:37:57 -0500

Pondicherry University, India

Walk in interview for guest faculty in Pondicherry University, India. For more information please visit http://www.bicpu.edu.in/bioinfor140814.pdf