BOL: Related items

WALK – IN – INTERVIEW @ Agricultural Knowledge Management Unit Indian Agricultural Research Institute, New Delhi-110012

Fri, 12 Dec 2014 21:33:02 -0600

Walk-in-interview for the following temporary positions will be conducted on 20th December 2014 (between 10:00 AM to 01:00 PM) at Agricultural Knowledge Management Unit, A0 block (Ground Floor), LBS Building, Indian Agricultural Research Institute, New Delhi-110012:

1 Dr. A.K.Mishra Coordinator & PI (BTISnet)

Traineeship (two) for one year

Rs. 5000/- (consolidated)

M.Sc. (Bioinformatics) with 60 % marks from a recognized University

20-12-2014 (10:00 AM -11:00 AM)

Studentship (four) for one year

Rs. 2500/- (consolidated)

Final year M.Sc./ M.Tech (Bioinformatics) Students from a recognized University

20-12-2014 (11:00 AM- 1:00 PM)

The positions are purely temporary and co-terminus with the DBT Programme. Eligible candidates are requested to submit the application form in the prescribed format along with original certificates/ documents (Degree, Marks sheets, Work experience, if any) at the time of interview. No TA/DA will be paid. Maximum age limit is 28 years for all positions. Age relaxation of 5 yrs for SC/ST and woman candidates and 3 years for OBC candidates will be given. Canvassing in any form invites disqualification.

Advertisement: http://www.iari.res.in/files/BIC-08122014-20141208-172344.pdf

Epiviz: an interactive visualization tool for functional genomics data.

Jit — Mon, 09 Jul 2018 05:27:39 -0500

Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can addd3 visualizations. You can see a video tour here.

https://bioconductor.org/packages/release/bioc/html/epivizr.html

https://github.com/epiviz

https://github.com/epiviz/epiviz

Address of the bookmark: https://epiviz.github.io/

Google Genomics

Tenzin Paul — Thu, 18 Dec 2014 11:05:42 -0600

Explore genetic variation interactively. Compare entire cohorts in seconds with SQL-like queries. Compute transition/transversion ratios, genome-wide association, allelic frequency and more.
Process big genomic data easily. Run batch analyses like principal component analysis and Hardy-Weinberg equilibrium on as many samples as you like, in minutes or hours, with just a little code.
Use Google's infrastructure and big data expertise. Store one genome or a million using Google Genomics and take advantage of the same infrastructure that powers Search, Maps, YouTube, Gmail and Drive.
Support emerging global standards. Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.

Address of the bookmark: https://cloud.google.com/genomics/

FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform

Neel — Fri, 10 Aug 2018 13:29:28 -0500

FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data. Given a BWT of the short-read sequencing data, FMLRC will build an FM-index and use that as an implicit de Bruijn graph. Each long read is then corrected independently by identifying low frequency k-mers in the long read and replacing them with the closest matching high frequency k-mers in the implicit de Bruijn graph. In contrast to other de Bruijn graph based implementations, FMLRC is not restricted to a particular k-mer size and instead uses a two pass method with both a short "k-mer" and a longer "K-mer". This allows FMLRC to correct through low complexity regions that are computational difficult for short k-mers.

Address of the bookmark: https://github.com/holtjma/fmlrc

Studentship at Nagaland University

Tue, 16 Dec 2014 01:35:00 -0600

Nagaland University
(A Central University Estd. By the Act of Parliament No. 35 of 1989)
Lumami 798 627, Nagaland
DBT Sponsored ‘Bioinformatics Infrastructure Facility’ Centre

Applications in plain paper are invited for the posts of (1) Traineeship (2 Nos.) and (2) Studentship – (2 Nos.) in the DBT funded-Bioinformatics Infrastructure Facility (BIF), Nagaland University, Lumami-798627, Nagaland. Details are given below. Interested candidates may submit the application along with self attested copies of certificates in support of the candidature to Prof. Chitta Ranjan Deb, Coordinator or Dr. L. N. Kakati, Deputy Coordinator, BIF Centre, Nagaland University, Lumami-798627, Nagaland on or before 15th January 2015.

The scanned application with relevant documents may be sent by email attachment to bifnulumami@gmail.com. Shortlisted candidates will be informed by email if called for interview. No TA/DA is admissible for attending the interview.

Traineeship (Two nos.)

Post Graduate degree in any branch of Life Sciences from UGC recognized Universities

Knowledge of computers and bioinformatics

Rs.8000/- p.m. fixed.

6 months

Studentship (Two nos.)

Pursuing Post Graduate degree in any branch of Life Sciences from UGC recognized Universities

Knowledge of computers and bioinformatics

Rs.8000/- p.m. fixed.

6 months

Terms and Conditions:

i) Applicants need to produce all original documents if call for interview.
ii) The posts are purely temporary and the appointment does not confer any entitlement or right over the job and will not be considered as formal service.
iii) No TA & DA will be paid for appearing in the walk-in-interview.
iv) The stipend/salary amount is subject to the sanction of DBT, New Delhi.

Advertisement: http://www.nagauniv.org.in/files/BIF%20Advt.pdf

SeqMonk:A tool to visualise and analyse high throughput mapped sequence data

Jit — Tue, 11 Sep 2018 04:39:38 -0500

SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic positions. It's main features are:

Import of mapped data from mapped data (BAM/SAM/bowtie etc)
Creation of data groups for visualisation and analysis
Visualisation of mapped regions against an annotated genome.
Flexible quantitation of the mapped data to allow comparisons between data sets
Statistical analysis of data to find regions of interest
Creation of reports containing data and genome annotation

Address of the bookmark: http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/

Senior Scientist (Agricultural Bio-informatics) (One post)

Wed, 24 Dec 2014 05:01:02 -0600

Agricultural Scientists Recruitment Board

Qualifications Essential:
Doctoral degree in Bio-informatics/ Biotechnology/Molecular Biology and Biotechnology/Life Sciences/ Computer Sciences with specialization in Bio-informatics including relevant basic sciences with 8 years’ experience in the relevant subject as Scientist/Lecturer or in an equivalent position in the Pay Band- 3 of 15600-39100 with Grade Pay of 5400/6000/7000/8000 having made contribution to research/teachin/extension education as evidenced by published work/innovations and impact.

Doctoral degree in the above subject(s) including relevant basic sciences with minimum 8 years’ experience of high quality post-doctoral research in an institution/organization as evidenced by at least 6 publications in journals with NAAS rating of 7.5 or above.

Desirable:
(i) Specialization and experience: Knowledge of software development and its application in crop bioinformatics, experience in handling ‘omies’data.
(ii) Teaching experience in relevant subject

The Secretary, Agricultural Scientists Recruitment Board, Indian Council of Agricultural Research Krishi Anusandhan Bhavan-I, Pusa New Delhi –110 012, India

Detailed eligibility criteria with how to apply information can be had at:
http://www.indiastudychannel.com/jobs/333467-Indian-Council-of-Agricultural-Research-looking-for-Assistant-Director-General.aspx

More at http://asrb.org.in/administrator/uploads_dir/1418978057english.pdf

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

Rahul Nayak — Thu, 04 Oct 2018 16:39:28 -0500

This is a tool for detecting structural variations using soft-clipping information From SAM files.

https://github.com/shinout/clipcrop

Address of the bookmark: https://github.com/shinout/clipcrop

RStudio

Jitendra Narayan — Sat, 27 Dec 2014 06:50:58 -0600

RStudio IDE is a powerful and productive user interface for R. It’s free and open source, and works great on Windows, Mac, and Linux.

The developers and expert trainers are the authors of several popular R packages, including ggplot2, plyr, lubridate, and others.

More at http://www.rstudio.com/

http://www.rstudio.com/products/RStudio/

Address of the bookmark: http://www.rstudio.com/

Hawkeye: an interactive visual analytics tool for genome assemblies

Abhimanyu Singh — Tue, 01 Jan 2019 11:56:17 -0600

Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies. Hawkeye is freely available and released as part of the open source AMOS project http://amos.sourceforge.net/hawkeye.

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-3-r34

Address of the bookmark: http://amos.sourceforge.net/wiki/index.php?title=Hawkeye