BOL: Related items

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

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.

Bioinformatics Project Fellow at Institute of Genomics & Integrative Biology - New Delhi, Delhi

Wed, 11 Mar 2015 03:04:38 -0500

Pay Scale: Rs. 16,000/- + 30 % HRA per month
Educational Requirements: M.Sc. in Bioinformatics with at least 55% marks Qualifications: Knowledge of Perl, R and other programming language or Database management or knowledge of pipelines to analyze NGS data or experience in scientific writing and good communication skills

Details will be available at: http://www.igib.res.in/sites/default/files/26032015.pdf

No of Post: 01, 01

How To Apply: 1. Please fill up the proforma 2. Candidate cannot apply for more than two posts. Last date of receiving application is 12-03-2015. No application would be entertained with “result awaited” status or after due date. List of shortlisted candidates will be put up on CSIR-IGIB website. No TA/DA will be paid to the candidates to attend the interview. The engagement shall be as per guidelines of CSIR/Funding agency. Candidates will have an option to give reply in Hindi. Note: The shortlisted candidates, have to report at 09:00 AM at Mall Road Campus, Delhi – 110007 on the day of interview along with any Photo ID card, (without photo ID card interview will not be conducted). 3 copies of updated signed C. V. (clearly mentioning Date of Birth and Hightest Qualification with percentage), Dissertation (if any), PhD thesis (if any) and original certificates/Self attested photocopies for verification.

General Instructions: Engagement is for the project and on behalf of the funding agency and the tenure shall be as mentioned above. The duration of the post is initially for One year or till the closing date of the project, whichever is earlier. Tenure may be extendable up to project duration. Contract may be terminated at any time by giving one-month notice by either side. The applicants will have no claim implicit or explicit for consideration against any CSIR/IGIB post. Candidates should note that non-fulfillment of the eligibility criterion will result in cancellation of candidature at any stage.

Last Date: 12-03-2015.
Age Limit: 28 Years

Research Associate Bioinformatics Central Institute for Research on Buffaloes (CIRB) - Hisar, Haryana

Fri, 31 Jul 2015 10:19:45 -0500

Research Associate (RA) under Network Project on Agricultural Bioinformatics

Name of the Project : Network Project on Agricultural Bioinformatics Number of positions One
Qualifications : Ph.D Degree in Bioinformatics/Biotechnology/ Biochemistry/Genetics & Breeding/Life Sciences OR Master’s Degree in relevant subject with at least 2 years research experience. Desirable : Working experience in Molecular Biology/Genomics/Bioinformatics, specifically, sequence data analysis using software’s proficiently

Emoluments : Masters Degree Holders Rs. 38,000/- per month Doctoral Degree Holders Rs. 40,000/- per month

Emoluments : Rs.25000/- per month for 1st and 2nd year and Rs. 28000/- per month for 3rd year
Age Limit : Upper age limit is 35 years for men and 40 years for women on the date of interview. Age relaxation for SC/ST and OBC candidates as per rules

More at http://www.cirb.res.in/attachments/195_walk-in-interview%20for%20contractual%20positions%20of%20RA%20and%20SRF%20%28On%20Dated%2011.8.2015%29.pdf

Summer Intern - Research Bioinformatics

Mon, 16 Feb 2015 12:26:32 -0600

Be proficient in LINUX, know perl or python, understand biology and Next Generation Sequencing.
The intern will port Agile Assay Design pipelines into Galaxy.
The intern will also learn to develope his/her own bioinformatics pipelines for PCR or NGS data analysis.

Who you are
You’re someone who wants to influence your own development. You’re looking for a company where you have the opportunity to pursue your interests across functions and geographies. Where a job title is not considered the final definition of who you are, but the starting point.

Qualifications:
Major: Bioinformatcis or biology major who is interested and wants to learn Biocomputing, At least 2 years of college.
Basic knowledge of LINUX and programming, e.g., perl, python, XML.

More at http://www.roche.com/careers/jobs/jobsearch/job.htm?id=E-00437679&locale=en&title=Summer%20Intern%20-%20Research%20Bioinformatics

BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data

Jit — Thu, 31 May 2018 09:35:23 -0500

BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a variant of the classical spectrum alignment algorithm introduced by Pevzner et al (2001). It uses an exhaustive search to find a k-mer path through a read that minimizes a heuristic objective function jointly considering penalties on correction, quality and k-mer support. This algorithm was first implemented in my fermi assembler and then refined a few times in fermi, fermi2 and now in BFC. In the k-mer counting phase, BFC uses a blocked bloom filter to filter out most singleton k-mers and keeps the rest in a hash table (Melsted and Pritchard, 2011). The use of bloom filter is how BFC is named, though other correctors such as Lighter and Bless actually rely more on bloom filter than BFC. https://github.com/lh3/bfc

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

A guide for complete R beginners :- Installing R packages

Archana Malhotra — Tue, 24 Feb 2015 20:23:34 -0600

Part of the reason R has become so popular is the vast array of packages available at the cran and bioconductor repositories. In the last few years, the number of packages has grown exponentially!

This is a short post giving steps on how to actually install R packages. Let’s suppose you want to install the ggplot2 package. Well nothing could be easier. We just fire up an R shell and type:
> install.packages("ggplot2")

In theory the package should just install, however:

if you are using Linux and don’t have root access, this command won’t work.
you will be asked to select your local mirror, i.e. which server should you use to download the package.

Installing packages without root access

First, you need to designate a directory where you will store the downloaded packages. On my machine, I use the directory /data/Rpackages/ After creating a package directory, to install a package we use the command:
> install.packages("ggplot2", lib="/data/Rpackages/") > library(ggplot2, lib.loc="/data/Rpackages/")

It’s a bit of a pain having to type /data/Rpackages/ all the time. To avoid this burden, we create a file .Renviron in our home area, and add the line R_LIBS=/data/Rpackages/ to it. This means that whenever you start R, the directory /data/Rpackages/ is added to the list of places to look for R packages and so:

> install.packages("ggplot2") > library(ggplot2)

just works!

Setting the repository

Every time you install a R package, you are asked which repository R should use. To set the repository and avoid having to specify this at every package install, simply:

create a file .Rprofile in your home area.
Add the following piece of code to it:

cat(".Rprofile: Setting UK repositoryn") r = getOption("repos") # hard code the UK repo for CRAN r["CRAN"] = "http://cran.uk.r-project.org" options(repos = r) rm(r)

I found this tip in a stackoverflow answer .

Bioinformatics Engineer -- Algorithm Development

Wed, 01 Apr 2015 21:39:05 -0500

Centrillion Biosciences is a venture backed life sciences company located in Palo Alto, California. The company provides high quality genomic services to academic and industrial customers including top universities and research institutes. Centrillion Biosciences has an immediate opening for a full-time Bioinformatics Engineer. We're looking for an energetic, innovative, and motivated person who works well independently and on teams. The ideal candidate will have experience designing and implementing efficient algorithms to process large datasets. The role will involve collaborating with research scientists and other engineers, so strong communication skills are a must.

Job Description

• Work within a fast-paced, collaborative environment with small project teams working on a variety of tasks ranging from new product development to DNA data processing
• Collaborate with Centrillion research scientists in order to bridge the gap between the laboratory and the digital world
• Develop tools to enable research projects to cope with the enormous amounts of data produced by modern DNA sequencing experiments
• Build simulation algorithms to help guide and analyze research done in the lab
• Solve challenging engineering problems that require the development of innovative algorithms

Requirements

• Strong background in mathematics/statistics with a degree in a related field
• Strong analytical, coding, communication, and organizational skills
• Experience with algorithm development, simulations, and data analysis
• Proficiency in at least one modern programming language (like Python or Perl)
• Experience analyzing genetic and biological data sets (e.g., DNA data analysis and image analysis)
• Experience with machine learning and pattern recognition is preferred

Please submit your resume at https://www.centrillionbio.com/career/ to apply for this position.