BOL: Related items

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.

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/

IIHR Recruitment 2015 – SRF, Project Asst & Research Associate Posts

Wed, 06 May 2015 06:13:26 -0500

IIHR Recruitment 2015 – SRF, Project Asst & Research Associate Posts: ICAR-Indian Institute of Horticultural Research (IIHR) has published a notification for the recruitment of Senior Research Fellow, Project Assistant and Research Associate vacancies on temporary basis. Eligible candidates may apply in prescribed application format on or before 15-05-2015. Other details like age, educational qualification, selection process, how to apply are given below…

IIHR Vacancy Details:
Total No. of Posts: 14
Name of the Post:
1. Senior Research Fellow: 12 Posts
2. Project Assistant: 01 Post
3. Research Associate: 01 Post

Age Limit: Candidates age limit is 40 years for men & 45 years for women for RA post, 35 years for men & 40 years for women for SRF post, 30 years for men & 35 years for women for JRF post and 21 to 40 years for Other as on closing date of receipt of applications. Age relaxation is applicable as per rules.

Educational Qualification: Candidates should possess M.Sc (Ag) Plant Pathology or Microbiology or Biotechnology or Biochemistry or M.Tech (Ag) or Bioinformatics for SRF Posts, 10th class with experience in workshop (welding fitting) for Project Asst Post and M.Sc (Ag) Plant Pathology or M.Sc (Ag) Biotechnology or Ph.D in Plant Pathology or Agricultural Biotechnology for RA Post.

Selection Process: Candidates will be selected based on their performance in interview.

How to Apply: Eligible candidates may send their application in the prescribed format along with attested copies of relevant certificates and should mention name of PI/ Co-PI, Item No. of the Post & name of the post clearly on the application as well as on the cover to the Concerned PI/ Co-PI, Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru-560089 on or before 15-05-2015 and attend the interview along with originals, two passport size photographs on 26 & 27-05-2015 from 10:00 AM Onwards.

Important Dates:
Last Date for Receipt of Applications: 15-05-2015.
Date & Time of Interview: 26 & 27-05-2015 from 10:00 AM Onwards.
Venue: IIHR Campus.

More at http://www.iihr.ernet.in/content/srf-jrf-application-format

KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation

Abhimanyu Singh — Wed, 12 Dec 2018 09:16:55 -0600

KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data by BLAST and GHOSTX searches, respectively, against a nonredundant set of KEGG GENES. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to the BlastKOALA server and can be executed in an interactive mode. See Step-by-step Instructions.

Reference: Kanehisa, M., Sato, Y., and Morishima, K. (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726-731. [pubmed] [pdf]

Address of the bookmark: https://www.kegg.jp/blastkoala/

BINC 2015 !!!

Rahul Nayak — Sat, 11 Apr 2015 20:35:27 -0500

Pondicherry University,Puducherry,on behalf of Department of Biotechnology, Government of India, will conduct the BINC examination in2015. The objective of this examination is to certify bioinformatics professionals, trained formally as well as self-trained.Registration will open from March 9,2015 to April 30,2015. Pondicherry University, Puducherry has been identified as a nodal agency by the Department of Biotechnology, Govt. of India to coordinate this examination along with nine centres namely, Pune University, Pune; Anna University, Chennai; Calcutta University, Kolkata; Institute of Bioinformatics & Applied Biotechnology, Bangalore; North-Eastern Hill University, Shillong, University of Hyderabad, Hyderabad; University of Kerala, Thiruvananthapuram; Jawaharlal Nehru University, New Delhi and Assam Agricultural University, Guwahati. In the BINC 2013 examination,17 candidates were certified. DBT has agreed to fund Research fellowships for all the BINC qualified Indian nationals to pursue Ph.D. in Indian Institutes/Universities. Note that the candidate must possess a postgraduate degree(or equivalent) & meet the criteria of the institutes/universities in order to avail research fellowship. In addition, cash prize of Rs. 10,000/- will be awarded to the top 10 BINC qualifiers.

More at http://www.binc.co.in/College/Index_New.aspx

BINC notification http://www.binc.co.in/PdfDocuments/Notification.pdf

Few dates to remember:

Starting of online submission of application: March 9, 2015
Last date for submission of application: April 30,2015
Examination consists of two parts:
Part I (Paper I) : June 7, 2015 (10 AM-12 PM)
Part II ( Paper II & III) :June 28, 2015 (9 AM-12 PM & 2 PM-4 PM)

Minipolish: A tool for Racon polishing of miniasm assemblies

BioStar — Tue, 03 Dec 2019 02:40:54 -0600

Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long reads.

Racon is a great polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it operates on FASTA files, not the GFA graphs that miniasm makes.

That's where Minipolish comes in. With a single command, it will use Racon to polish up a miniasm assembly, while keeping the assembly in graph form.

It also takes care of some of the other nuances of polishing a miniasm assembly:

Adding read depth information to contigs
Fixing sequence truncation that can occur in Racon
Adding circularising links to circular contigs if not already present (so they display better in Bandage)
'Rotating' circular contigs between polishing rounds to ensure clean circularisation

Address of the bookmark: https://github.com/rrwick/Minipolish

Karpagam University, Coimbatore, of Sr. Prof, Prof, Associate and Assistant Professors Karpagam University, Coimbatore - Coimbatore, Tamil Nadu

Thu, 16 Apr 2015 00:30:45 -0500

Karpagam University, Coimbatore, Recruitment of Sr. Prof, Prof, Associate and Assistant Professors

Name of the College: Karpagam University, Coimbatore

Date of official publication: 15th April 2015

The newspaper wherein this job advertised: The Hindu Newspaper

Name of the posts: Senior Professors, Professors, Associate Professors and Assistant Professors

Departments:
Bioinformatics
Biotechnology
Qualifications/Eligibility: The candidates should have qualifications as M.E/M.Tech/M.A/M.Com/MBA/M.Sc/M.Phil/NET/SLET/Ph.D

Job Location: Coimbatore, TN

Salary: As per college norms

How to apply: Interested and eligible candidates are requested to apply online at http://www.karpagamuniversity.edu.in/career

Last date: As soon as possible from 15th April 2015

Reference: The Hindu Newspaper dated 15-04-2015, Coimbatore edition on 14th page

Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny

Jit — Mon, 17 Feb 2020 05:38:46 -0600

Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to identify scaffolds that have been incorrectly assembled according to the genetic map, and split those scaffolds.

Address of the bookmark: http://catchenlab.life.illinois.edu/chromonomer/

BINC Sample Question Paper !!!

Jitendra Narayan — Thu, 16 Apr 2015 09:16:18 -0500

BINC sample question paper. Wish you all the best for BINC examination.

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

Jit — Mon, 18 May 2020 10:53:32 -0500

Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately (see Usage).

Address of the bookmark: https://github.com/dutilh/CAT