BOL: Related items

Phytozome v12.1: plant science community hub for accessing palnts genomic data

Surabhi Chaudhary — Tue, 17 Mar 2020 07:30:17 -0500

Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere. As of release v12.1.6, Phytozome hosts 93 assembled and annotated genomes, from 82 Viridiplantae species. More than half of these genomes have been sequenced, assembled and/or annotated with JGI Plant Science program resources. By integrating this large collection of plant genomes into a single resource and performing comprehensive and uniform annotation and analyses, Phytozome facilitates accurate and insightful comparative genomics studies.

Address of the bookmark: https://phytozome.jgi.doe.gov/pz/portal.html

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

Flanker

Rahul Nayak — Sat, 27 Feb 2021 22:04:53 -0600

Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence.

Address of the bookmark: https://github.com/wtmatlock/flanker

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).

IVA: accurate de novo assembly of RNA virus genomes

Neel — Wed, 23 Jun 2021 07:51:59 -0500

IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from human immunodeficiency virus-1 or influenza-virus-infected people and demonstrated that IVA outperforms all other virus de novo assemblers.

Availability and implementation: The software runs under Linux, has the GPLv3 licence and is freely available from http://sanger-pathogens.github.io/iva

https://pubmed.ncbi.nlm.nih.gov/25725497/

Address of the bookmark: https://github.com/sanger-pathogens/iva

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

Illumina based assembly pipeline steps !

Surabhi Chaudhary — Fri, 10 Dec 2021 06:22:54 -0600

Illumina

Merge re-sequenced FastQ files (cat)
Read QC (FastQC)
Adapter trimming (fastp)
Removal of host reads (Kraken 2; optional)
Variant calling
1. Read alignment (Bowtie 2)
2. Sort and index alignments (SAMtools)
3. Primer sequence removal (iVar; amplicon data only)
4. Duplicate read marking (picard; optional)
5. Alignment-level QC (picard, SAMtools)
6. Genome-wide and amplicon coverage QC plots (mosdepth)
7. Choice of multiple variant calling and consensus sequence generation routes (iVar variants and consensus; default for amplicon data || BCFTools, BEDTools; default for metagenomics data)
  - Variant annotation (SnpEff, SnpSift)
  - Consensus assessment report (QUAST)
  - Lineage analysis (Pangolin)
  - Clade assignment, mutation calling and sequence quality checks (Nextclade)
  - Individual variant screenshots with annotation tracks (ASCIIGenome)
8. Intersect variants across callers (BCFTools)
De novo assembly
1. Primer trimming (Cutadapt; amplicon data only)
2. Choice of multiple assembly tools (SPAdes || Unicycler || minia)
  - Blast to reference genome (blastn)
  - Contiguate assembly (ABACAS)
  - Assembly report (PlasmidID)
  - Assembly assessment report (QUAST)
Present QC and visualisation for raw read, alignment, assembly and variant calling results (MultiQC)

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

Interactive Market Intelligence

Pranjali Yadav — Mon, 19 Jan 2015 08:20:38 -0600

BioInformatics LLC, a premier research and advisory firm serving the life science industry, has launched groundbreaking, dynamic-data presentation platform, Interactive Market Intelligence— the only cloud-based market research analytics tool for the life science tools industry.

Superior to traditional PDF and PowerPoint reports, Interactive Market Intelligence allows end-users to filter, create and export literally thousands of views of data — all easily obtainable from a set of core metrics that include market, brand, customer and workflow analytics in well-defined segments of the life science market.

The Market for Real-Time PCR is the first in a series of topics to be explored using the Interactive Market Intelligence platform. The primary research analysis is based on a survey of 900+ international scientists performing qPCR in their laboratories.

Key data findings from "The Market for Real-Time PCR": Global market for qPCR in 2015 is estimated to be $3.6B; The average growth in qPCR throughput is expected to be at 9.8% in 2015; 22% of respondents are highly likely to switch primary suppliers of qPCR products; 50% of respondents use pre-designed primer/probe sets.