BOL: Related items

VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules

Rahul Nayak — Thu, 04 Oct 2018 16:30:44 -0500

VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store only those read-pairs or reads who intersect some region around the variant locations. Alternatively, if your scientific question is focused on only one aspect of the data (e.g. breakpoints), many reads can be removed without losing the information relevant to the problem.

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

Bioinformatics Scientist at ICAR Labs

Sun, 21 Dec 2014 23:47:03 -0600

AGRICUL AGRICULTURAL SCIENTISTS RECRUITMENT BOARD TURAL SCIENTISTS RECRUITMENT BOARD
KRISHI ANUSANDHAN BHAVAN-I, PUSA, NEW DELHI-110 012

ADVERTISEMENT NO. 03/2014

PRINCIPAL SCIENTIST

Pay Band: Minimum pay of `43,000 in the PB-4 of `37400-67000/- + RGP of `10,000/-.

Age: The candidates must not have attained the age of 52 years as on 19.01.2015. There shall be no age limit for the Council’s employees.

ICAR-Indian Institute for Agricultural Biotechnology, (IIAB) Ranchi (Jharkhand)

151. Principal Scientist (Bioinformatics) (One post)

SENIOR SCIENTIST/PROGRAMME COORDINATOR

Pay Band: PB-4 of ` 37400-67000/- + RGP of ` 9,000/-.

Age: The candidates must not have attained the age of 47 years as on 19.01.2015. There shall be no age limit for the Council’s employees.

National Institute of Biotic Stress Management, Raipur (Chhattishgarh)

166. Senior Scientist (Bioinformatics) (One post)

IMPORTANT NOTE
I. (i) CLOSING DATE

THE CLOSING DATE FOR RECEIPT OF APPLICATIONS IN AGRICULTURAL SCIENTISTS RECRUITMENT BOARD IS 19.01.2015 (For applications posted from abroad and in the Andaman and Nicobar Islands, Lakshdweep, Minicoy and Amindivi islands, States/ Union Territories in the North-Eastern Region, Ladakh Division of J & K State, Sikkim, Pangi, Sub-division of Chamba, Lahul and Spiti Districts of Himachal Pradesh, the last date for receipt of application will be 02.02.2015). Non receipt of the application by the closing date will result in rejection of the application.

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

NanoPack: visualizing and processing long-read sequencing data

Jit — Tue, 25 Dec 2018 21:20:50 -0600

The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.

Address of the bookmark: https://github.com/wdecoster/nanopack

ShRec3D

Jitendra Narayan — Thu, 25 Dec 2014 23:14:52 -0600

ShRec3D is a program that aims at reconstructing a genome 3D structure (b) from the sole knowledge of the contacts between different genomic regions (a) as determined by Hi-C (http://www.ncbi.nlm.nih.gov/pubmed/19815776).

There are two options to run ShRec3D (on linuX only so far): the first one uses the Matlab complier runtime environment (MCR), the second one doesn't need any other library to be installed but only works with the latest versions of Linux (equivalent to Fedora 19 and above).

Address of the bookmark: https://sites.google.com/site/julienmozziconacci/#TOC-Downloads

ngs-bits - Short-read sequencing tools

Neel — Thu, 16 Jan 2020 23:14:00 -0600

Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources:

Binaries for Linux/macOS
From sources for Linux/macOS
From sources for Windows

Address of the bookmark: https://github.com/imgag/ngs-bits

Which of the followings are the best place to study Bioinformatics ?

Reshma Khatun — Sun, 28 Dec 2014 00:20:30 -0600

Bioinformatics is a major growth area and qualified Bioinformaticians are in high demand. An explosion in biological data has resulted from genome projects, next generation sequencing and other 'omics' techniques. Bioinformatics provides the tools to analyse and exploit such data sets.

Can you please suggest me the best place to study bioinformatics ( Grad/PostGrad).

Understanding your reads and mapping !

Neel — Wed, 29 Jan 2020 06:29:55 -0600

One of the best tutorial for beginners ...

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

Roche has acquired Bina Technologies !!!

Jit — Tue, 30 Dec 2014 09:42:16 -0600

Bina Technologies is a privately held company that provides a big data platform for centralized management and processing of next generation sequencing (NGS) data for the academic and translational research markets. Bina will be integrated into the Roche Sequencing Unit, and will continue to focus on development of their innovative genomic analysis solution.

Roche has acquired Bina Technologies, a privately-owned biotech company based in California. The biotech’s first product was the Bina Box, a platform for secondary genomic analysis, sequence alignment, and variant calling, but since 2012, it has developed other products and platforms.

It is our shared vision with Roche that informatics and data sciences are critical elements of an end-to-end genomics solution. Fast, easy-to-use, scalable, and robust informatics solutions make a big difference in the quality and impact of the work of scientists and researchers. We believe in the future of data-driven, personalized medicine. We are passionate about accelerating that future together with Roche.

Financial details of the deal were not disclosed. For Roche, the move is yet another in a string of acquisitions. Last week (December 18), Roche paid $489 million for antibody maker Dutalys. And earlier this month, Roche bought prenatal testing company Ariosa Diagnostics.

Reference

http://blog.bina.com/news/bina-technologies-acquired-by-roche?&__hssc=109677338.1.1419953400266&__hstc=109677338.b8350f2729889b08f1325906d5236cd3.1419953400266.1419953400266.1419953400266.1&hsCtaTracking=96cac941-9372-4bbf-bacb-3ca6f1ff8cfd|3fce0f18-835b-4086-9345-388880861732

http://www.the-scientist.com/?articles.view/articleNo/41750/title/Roche-Buys-Bioinformatics-Firm/

Type Hinting

Pranjali Yadav — Fri, 09 Jan 2015 22:26:13 -0600

Python creator Guido van Rossum’s proposal for static type-checking annotations is inching closer to reality, and the feature has taken on a new name: type hinting.

Back in August, van Rossum published a proposal on the Python mailing list recommending type-checking annotations as a valuable feature for the next version of Python to improve the performance of editors and IDEs, linter capabilities, standard notation, and refactoring. Van Rossum’s latest proposal, posted late last month, outlined plans to publish a Python Enhancement Proposal (PEP) in early January to put the feature now known as type hinting on track for inclusion in Python 3.5, slated for release this September.

Reference

https://quip.com/r69HA9GhGa7J

Postdoctoral Researcher in Cancer Systems Biology

Mon, 12 Jan 2015 01:44:11 -0600

Postdoctoral Researcher in Cancer Systems Biology
Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford
Grade 7: £30,434 - £37,394 with a discretionary range to £40,847 p.a.
Applications are invited for a Postdoctoral Researcher in Cancer Systems Biology to join a rapidly developing Bioinformatics Research Core group headed by Dr Anastasia Samsonova. The purpose of the role is to develop and deliver integrative approaches to dissect the complexity of cancer as a genomic disease. The research will focus on development and application of effective strategies for mining and integration of complex human *omics datasets and clinical/phenotypic data in cancer studies.

The role sits at the critical interface between genetics and cancer systems biology, and would suit a candidate who is interested in developing a career at the confluence of Statistics/Data Mining/Machine Learning and Biology. Ideally, you will have experience in development of analytical approaches to high-throughput and multivariate data mining and integration gained through a PhD (or equivalent) in a quantitative subject (eg mathematics, statistics, physics, engineering or computer science).

Experience of statistics and/or machine learning techniques is highly desirable as is evidence of prior experience of developing bioinformatics software and/or analysing complex *omics data sets. You will be able to work as part of a team and independently and deliver results to the required standard and schedule. You should be able to organise and prioritise your own work, as well as have excellent communication skills, both written and oral. The post will involve interactions with collaborators from such diverse fields as applied mathematics, statistics, computer science and medicine.

This is a full-time post, fixed-term until 31 March 2017. For informal enquiries, contact Dr Anastasia Samsonova (bioinformatics@oncology.ox.ac.uk).

All applicants must complete a short application form and upload a CV and supporting statement.

The closing date for applications is 12.00 noon on 26 January 2015.

More at https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.display_form