BOL: Related items

pybedtools

Shruti Paniwala — Wed, 20 Aug 2014 01:03:41 -0500

pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs (https://github.com/arq5x/bedtools), which are widely used for genomic interval manipulation or "genome algebra". pybedtools extends BEDTools by offering feature-level manipulations from with Python. See full online documentation, including installation instructions, at http://pythonhosted.org/pybedtools/.

More at http://pythonhosted.org/pybedtools/

A powerful toolset for genome arithmetic.http://code.google.com/p/bedtools/

PSPairwise Sequentially Markovian Coalescent (PSMC) model

Jit — Thu, 19 Apr 2018 05:29:23 -0500

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Address of the bookmark: https://github.com/lh3/psmc

NGS Platforms launched by BGI’s MGI Tech

Jit — Thu, 10 Jan 2019 04:42:06 -0600

MGI Tech Co., Ltd. (MGI), a subsidiary of BGI Group, is committed to enabling effective and affordable healthcare solutions for all. Based on its proprietary technology, MGI produces sequencing devices, equipment, consumables and reagents to support life science research, medicine and healthcare. MGI's multi-omics platforms include genetic sequencing, mass spectrometry and medical imaging. Providing real-time, comprehensive, life-long solutions, its mission is to develop and promote advanced life science tools for future healthcare.

MGI, a subsidiary of global genomics leader BGI Group, announced pricing and its first early access customer for the new ultra high-throughput sequencer, MGISEQ-T7, saying it has driven down sequencing cost to $5 per gigabyte, with exceptionally high accuracy. Such innovations are helping more people to realize the benefits of genomic information.

In October, MGI launched the MGISEQ-T7, a highly flexible production-scale platform that is the most powerful sequencer to date. It can produce as many as 60 whole human genomes in one day. The instrument sells for $1 million.

The T7 enables simultaneous but independent operation of up to four flow cells, which means different applications such as single-cell RNA sequencing, whole exome sequencing and whole genome sequencing can be run in different flow cells at the same time. This helps to reduce costs, allowing MGI to offer the most competitive sequencing price in the market.

Powered by DNBseq™, MGISEQ delivers quality data with accuracy for SNP and Indel calling rate of 99.9% and 99%, respectively, along with decreased duplication rate down to less than 2 percent, and almost zero Index mis-assignment rate.

SOURCE MGI

https://www.bgi.com/global/company/news/bgis-mgi-tech-launches-two-new-ngs-platforms/

http://en.mgitech.cn/

Bioinformatics JRF/SRF position at IARI

Thu, 04 Sep 2014 04:14:01 -0500

DIVISION OF NEMATOLOGY
INDIAN AGRICULTURAL RESEARCH INSTITUTE
NEW DELHI 110012
Applications are invited for the posts of one Junior
Research Fellow and one RA in the DBT funded project entitled “ Plant parasitic nematode genome informatics - insilico resource development”. The project is for a period of three years.

Essential qualifications for JRF
: M. Sc. in Bioinformatics with experience in Proteomics, genomics and structural biology. Knowledge of programming language, pearl and database – HTML, CSS,php and Java script.
Essential qualifications for Research Associate:
MSc/MTech in Bioinformatics with three years experience or Ph.D in Bioinformatics with experience in proteomics, genomics and structural biology. Knowledge of programming language, perl and database
– HTML, CSS, Java script. NGS sequence assembly and analysis and algorithm designing.
Age limit : 35 years maximum (5 year relaxation for SC/ST and women candidates)
Emoluments:
JRF: 16,000 + 30% HRA
.
Res Assoc: Rs22,000 + 30% HRA
The post is purely temporary in nature and is co-terminus with the project. The appointment would be initially for one year and may be extended further upon satisfactory performance.
Interested candidates
should send the duly filled application forms (format in the following page ) so as to reach on or before 20.9.2014 along with all the relevant documents.

More at http://www.iari.res.in/files/JRF_RA-03092014-20140903-135319.pdf

Nucleus: Python and C++ code for reading and writing genomics data.

Jit — Sun, 02 Feb 2020 08:14:19 -0600

Nucleus is a library of Python and C++ code designed to make it easy to read, write and analyze data in common genomics file formats like SAM and VCF. In addition, Nucleus enables painless integration with the TensorFlow machine learning framework, as anywhere a genomics file is consumed or produced, a TensorFlow tfrecords file may be used instead.

Address of the bookmark: https://github.com/google/nucleus

URDIP Pune Bioinformatics SRF/PA Openings

Sat, 20 Sep 2014 20:48:50 -0500

CSIR UNIT FOR RESEARCH AND DEVELOPMENT OF INFORMATION PRODUCTS
NCL Campus, S.No.113,114, Pashan, Pune 411 008

ADVERTISEMENT NO. - URDIP/ 5/2014

Learning opportunity for young Science and Engineering professionals to make a career in Information Science Industry CSIR has set up a Unit for Research and Development of Information Products (CSIR-URDIP) at Pune to work in the area of Scientific Informatics (ChemBioinformatics/Patent Informatics/Phytoinformatics/Toxinformatics) and related
software development projects.

Applications are invited from CSIR - UGC NET Qualified Candidates for consideration as Project Fellow (PF) and/or Senior Project Fellow (SPF) based on the experience to work on existing and new projects at CSIRURDIP.

Project Fellow

Remuneration - (Rs. 16,000.00 + 20% HRA)

M. Sc. In Biochemistry/Microbiology/Bioinformatics [Post-code A02] only with minimum of 55% marks

Senior Project Fellow

Remuneration - (Rs. 18,000.00 + 20% HRA)

M. Sc. in Biochemistry/Microbiology/Bioinformatics [Post-code A05] only with minimum of 55% marks plus two years research or relevant informatics experience

Please visit www.urdip.res.in/career.htm to apply online by 30th September, 2014.

Successful candidates who have appeared for NET exam in 2012 and 2013 are only eligible to apply.

Advertisement: http://115.112.95.114/urhr/download/Advt5_2014.pdf

Bioinformatics SVIMS Project Assistant Walk IN

Sat, 20 Sep 2014 21:02:29 -0500

SRI VENKATESWARA INSTITUTE OF MEDICAL SCIENCES
TIRUPATI, ANDHRA PRADESH, INDIA- 517 507
BIOINFORMATICS CENTRE, DEPARTMENT OF BIOINFORMATICS

Eligible candidates are invited for a walk-in-interview for recruitment of Project Assistant in SVIMS Bioinformatics centre under the BTISnet Project entitled “Creation of Bioinformatics Infrastructure Facility for promotion of Biology teaching through Bioinformatics” on 25.09.2014 at 11 AM in SVIMS, Tirupati. The engagement will be made purely on temporary basis for a period of one year and it can be terminated at any time without notice or without assigning any reason thereof by the Coordinator of the Project. The person engaged shall not be entitled for any claim implicit or explicit for absorption in the University.

1. Name of the post : Project Assistant

2. Qualification :
i) Essential : MSc Bioinformatics/MTech (Biotechnology/Bioinformatics)

ii) Desirable : Experience in Bioinformatics research work (Preference will be given to candidates qualified in BINC/UGC/CSIR/NET/GATE)

3. Remuneration : 16000 + 10% HRA for NET/GATE candidates 14000 + 10% HRA for M. Tech / M.Sc. Candidates

4. Place of posting : Tirupati

5. Duration of the Project : One year

Terms and conditions:

1. Candidates are required to submit the Biodata relevant certificates in support of their age and educational qualification etc., before the interview committee, SVIMS University, Tirupati.

2. Candidates called for interview will attend the interview at their own cost.
3. Interim enquiries will not be entertained.
4. The maximum age limit for Project Assistant is 28 years for general category and 33 years for SC and ST category candidates as on 25th September, 2014.

http://svr98.ehostpros.com/~svimsb98/Project%20Assistant_notification.pdf

Nieduszynski Group

Fri, 26 Sep 2014 19:35:06 -0500

Complete, accurate replication of the genome is essential for life. All chromosomes in eukaryotic cells must be duplicated and then segregated to daughter cells to ensure genetic integrity and produce the large number of cells that make up a multicellular organism. We are using genetic, genomic and computational methods to understand how chromosome replication is regulated to ensure genome stability. By focusing on the basic biology that underpins cell growth and division we aim to provide new insights that may help our understanding of diseases such as cancer and congenital disorders.

More http://www.nieduszynski.org/index.php
http://www.path.ox.ac.uk/research/cell-biology-and-pathology/conrad-nieduszynski-group

The Home Microbiome Project

Tue, 02 Sep 2014 15:21:49 -0500

The Home Microbiome Project is an initiative aimed at uncovering the dynamic co-associations between people's bacteria and the bacteria found in their homes.The hope is that the data and project will show that routine monitoring of the microbial diversity of your body and of the environment in which you live is possible. Computer animation courtesy the Biology & Built Environment (BioBE) Center, University of Oregon and Cameron Slayden at Cosmocyte. http://vimeo.com/90059732 BioBE on Vimeo: http://vimeo.com/user22991553

Mercator: Multiple Whole-Genome Orthology Map Construction

Jit — Tue, 19 May 2020 16:46:22 -0500

Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an ancestral genome. However, it has been pointed out that this use of the term is incorrect (Passarge et al. 1999) and thus we will use the terms "homologous", "orthologous", and "paralogous" instead. Ideally, given K genomes, we would like to identify all orthologous genomic regions as well as paralogous regions within each genome and hypothetical ancestral genome. Maps listing these relationships are extremely valuable to researchers performing comparative analyses of genomic sequence. Here we present our initial work in the form a program called Mercator that constructs orthology maps between multiple whole genomes.

Address of the bookmark: https://www.biostat.wisc.edu/~cdewey/mercator/