BOL: Related items

CGView - Circular Genome Viewer

Jit — Mon, 19 Sep 2016 07:52:26 -0500

GView is a Java package used to display and navigate bacterial genomes. GView is useful for producing high-quality genome maps for use in publications and websites, or as a visualization tool in a sequence annotation pipeline. Users can interact with the genome using a powerful pan-and-zoom interface, or GView can write static images of a genome to a file. GView can draw a genome using either circular or linear layouts. For examples of some of the images GView can produce, see the Image Gallery. GView is a re-write of CGView, a circular genome viewer written by Paul Stothard. The goal of GView is to provide greater user interaction, and more flexibility in how the genome map is rendered. To aid with easily configuring the display of a genome, a style editor has been included to provide an intuitive, user-friendly graphical user interface for customizing genome maps. Styling attributes such as colours or fonts for the various map elements can be adjusted in real time. Customized styles can be saved for later use or for application to other genome maps using GView's custom file format.

Address of the bookmark: http://wishart.biology.ualberta.ca/cgview/

BLAST Ring Image Generator (BRIG)

Anjana — Fri, 30 Sep 2016 09:18:50 -0500

BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at: http://sourceforge.net/projects/brig

If you have any questions or comments, post them on one of the trackers on BRIG’s SourceForge page: http://sourceforge.net/tracker/?group_id=328245.

Features:

Images show similarity between a central reference sequence and other sequences as concentric rings.
BRIG will perform all BLAST comparisons and file parsing automatically via a simple GUI.
Contig boundaries and read coverage can be displayed for draft genomes; customized graphs and annotations can be displayed.
Using a user-defined set of genes as input, BRIG can display gene presence, absence, truncation or sequence variation in a set of complete genomes, draft genomes or even raw, unassembled sequence data.
BRIG also accepts SAM-formatted read-mapping files enabling genomic regions present in unassembled sequence data from multiple samples to be compared simultaneously

Address of the bookmark: http://brig.sourceforge.net/

Junior Research Fellow at Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram

Mon, 07 Nov 2016 10:27:06 -0600

Adv. # 22/ 2016
Applications are invited from suitable candidates for one position of Junior Research Fellow in a DST funded bioinformatics research project entitled "Major gene influxes in microbial genome evolution" in the Laboratory of Dr. Shijulal Nelson-Sathi at Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram.

ESSENTIAL QUALIFICATIONS:
We are looking for a motivated candidate with keen interest in bioinformatics and microbial genome evolution. The candidate must have a Master’s Degree in Bioinformatics, Computational Biology, Computer Science, Microbiology, Biology or a related field with good academic record.

DESIRABLE QUALIFICATIONS
Hands on research experience on handling next generation sequencing data and phylogenetic reconstruction methods. Excellent programming skills (Perl/Python/Java/Php) and experience in working on Unix/Linux platform is preferred. Furthermore; good knowledge is required in statistics (R/Matlab) and the application of bioinformatics analysis tools.

AGE:
Below 28 years as on 15th November, 2016.

EMOLUMENTS:
Rs. 25,000 + 20% HRA for NET/GATE qualified and Post Graduate in Professional Degree course qualified candidates and
Rs. 12,000/- + 20% HRA for others.

DURATION:
Initial appointment will be given for one year and further extension will be based on the performance till termination of the project.
Only those fulfilling the above criteria need apply and will be called for interview. In the event of more than 10 candidates being short-listed by screening the applications, a written test will be conducted before the selection interview and only those who are successful in the written test will be interviewed. No TA/ DA will be given for appearing in the interview.

Suitably qualified candidates may send applications in the prescribed format (Download here) with a photograph, a copy of full resume indicating the percentage of Marks obtained and attested photocopies of credentials & experience to reach the undersigned on or before 15th November, 2016. Envelopes must be superscripted with abbreviated title of the project, advertisement number and job title. Selection to the position will not entitle the candidate to any future positions at RGCB (permanent or otherwise). As with all project positions at RGCB, the position will be co terminus with end of the project.

RA Bioinformatics at School of Computational & Integrative Sciences, JNU, India

Fri, 18 Nov 2016 03:57:56 -0600

School of Computational & Integrative Sciences
Jawaharlal Nehru University
New Delhi – 110067

Date: Nov 11th. 2016 Last Date: Nov 25th. 2016

PROJECT ID: 632

The following posts are urgently required to be filled for the Department of Biotechnology, Government of India funded project entitled "Computational Core for Plant Metabolomics" administrated by Prof Indira Ghosh, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110 067

NB:For all Bioinformatics posts, preference will be given to candidates with a good knowledge of Python and/or R. Knowledge of JAVA will also get a special consideration.

RA / Research Associate (Metabolic engineering/Computational Biologist)

Salary: Rs. 36000/- + HRA
Vacancy: 1
Essential Qualifications: PhD in Bioinformatics /Mathematics/Computer Science with experience in analyzing high throughput omics-based data/ system Biology/ Analysis of Network Biology. Published paper in the field is a must to prove the experience.
Desired Skills: Prior experience in handling and guiding bioinformatics, metabolomics data, planning of new research area in metabolic driven network , managing the project portal, preparing and filing reports etc. Will be expected to communicate with user groups and coordinate with LIMS group in Hyderabad and the Cheminformatics group in Delhi.

RA / Research Associate (Chemo-informatics/Computational Biologist)

Salary: Rs. 36000/- + HRA
Vacancy: 1
Essential Qualifications: PhD in Bioinformatics/ computational biology/ Biophysics/Computer Science. Computational and Chemical structure related experience is a necessary qualification proven by paper published and program developed.
Desired Skills: Research experience in Chemical scaffold mapping, in silico Spectral analysis, Biological Database Designing & Integration is required. Individual is responsible to develop methods related to metabolite identification, Testing and refining and integrate LIMS with IIIT Hyderabad and will be expected to communicate with user groups.

Project SRF (Bioinformatics/Programming)

Salary: As per DBT rules
Vacancy: 1
Essential Qualifications: Masters/B Tech in Basic Sciences with at least 2yrs of research experience in Bioinformatics/Computational Biology related to Database /portal building & maintenance ,high throughput data handling and analysis etc. For M.Sc/B.Tec, Published paper in peer-reviewed Journal and for M.Tech, thesis submission in computational biology is a must.

More at http://www.jnu.ac.in/Career/currentjobs.htm

bipype

Jit — Thu, 01 Dec 2016 08:47:38 -0600

Bipype is a very useful program, which prepare a lot of types of bioinformatics analyses. There are three input options: amplicons, WGS (whole genome sequences) and metatranscriptomic data. If amplicons are input data, then bipype does reconstruction and pairs merging. After that biodiversity is searching. There are two types of searching depending on the amplicons types (ITS or 16S). If WGS are chosen, then bipype finds the SA coordinates of the input reads and generates alignments in the SAM format given single-end reads, aligns reads to reference sequence(s). All of these analyses will be shown with Krona program, which allows to show hierarchical data with pie charts.

Address of the bookmark: https://readthedocs.org/projects/bipype/

MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation

Neel — Thu, 15 Dec 2016 05:47:35 -0600

MyPro is an improved genomics software pipeline for prokaryotic genomes. MyPro is user-friendly and requires minimal programming skills. High-quality prokaryotic genome assembly and annotation can be obtained with ease. It performed better than de novo assemblers and contig integration software. Produces more contiguous assemblies, higher N50 values and lower number of contigs.

More at https://sourceforge.net/projects/sb2nhri/files/MyPro/

Address of the bookmark: http://www.sciencedirect.com/science/article/pii/S0167701215001207

Bioinformatics Contest 2017!

Neel — Fri, 23 Dec 2016 14:03:37 -0600

Bioinformatics Contest 2017! Rosalind is co-organizer.
Compete with thousands of people worldwide on bioinformatics problem solving.
Everything is online. Qualification round starts on January 23, 2017. Final is on Feb 18.

You will need to solve bioinformatics problems using programming. The goal is to correctly solve as many problems as possible within 24 hours. Some of them will be approximation problems and will have partial grades. All rounds will be held online, submissions will be auto-graded in real time.

Check more at http://contest.bioinf.me/

Good luck!

Studentship

Tue, 24 Jan 2017 04:26:14 -0600

Advt. No. ACBR/BTBI/BIF/Manpower/ADV/16-17
Research Associate/ Studentship/ Traineeship Jobs opportunity in University of Delhi - Dr. B.R. Ambedkar Center for Biomedical Research (ACBR) on temporary basis
Studentship
No. of Post : 01
Qualifications : Applicants who are pursuing Post Graduate Degree course/ Diploma in Bioinformatics/ Biomedical Sciences/ Biotechnology/Life Sciences/Chemistry/ Biochemistry with a programme in Bioinformatics to carry out the project.
Remuneration : Rs. 8,000/-
Traineeship
No. of Post : 01
Qualifications : Applicants who have completed their Post Graduate degree in Bioinformatics /Biomedical Sciences/Biotechnology/Life Sciences/Chemistry/Biochemistry or any other branch of Life Sciences with knowledge in Bioinformatics
Remuneration : Rs. 8,000/-
Research Associate
No. of Post : 01
Qualifications : Ph.D. in Bio-Medical Sciences/Bioinformatics/ Biotechnology/Life Sciences/ Chemistry/ Bio-Chemistry and related areas
Remuneration : Rs. 36,000/-

Applicant are required to bring applications on plain paper, stating the name, address, date of birth. educational qualifications and experiences and Institute, along with attested photocopies of mark sheets and certificates etc. at the time of Interview. Applications should also be sent by Entail to Dr. Madhu Chopra, Coordinator, BIF Facility. Email: acbrdu.blisnet@nic.in; mchopradu@gmail.com.
Interview Date : 13.02.2017
Time : 10:00 am-12:00 noon
Venue : ACBR

Many-Core Engine (MCE) for Perl example

Jit — Tue, 31 Jan 2017 05:37:50 -0600

MCE spawns a pool of workers and therefore does not fork a new process per each element of data. Instead, MCE follows a bank queuing model. Imagine the line being the data and bank-tellers the parallel workers. MCE enhances that model by adding the ability to chunk the next n elements from the input stream to the next available worker.

CORE MODULES

Three modules make up the core engine for MCE.

MCE::Core: Provides the Core API for Many-Core Engine. The various MCE options are described here.
MCE::Signal: Temporary directory creation, cleanup, and signal handling.
MCE::Util: Utility functions for Many-Core Engine.

MCE EXTRAS

There are 4 add-on modules for use with MCE.

MCE::Candy: Provides a collection of sugar methods and output iterators for preserving output order.
MCE::Mutex: Provides a simple semaphore implementation supporting threads and processes.
MCE::Queue: Provides a hybrid queuing implementation for MCE supporting normal queues and priority queues from a single module. MCE::Queue exchanges data via the core engine to enable queuing to work for both children (spawned from fork) and threads.
MCE::Relay: Enables workers to receive and pass on information orderly with zero involvement by the manager process while running.

MCE MODELS

The models take Many-Core Engine to a new level for ease of use. Two options (chunk_size and max_workers) are configured automatically as well as spawning and shutdown.

MCE::Loop: Provides a parallel loop utilizing MCE for building creative loops.
MCE::Flow: A parallel flow model for building creative applications. This makes use of user_tasks in MCE. The author has full control when utilizing this model. MCE::Flow is similar to MCE::Loop, but allows for multiple code blocks to run in parallel with a slight change to syntax.
MCE::Grep: Provides a parallel grep implementation similar to the native grep function.
MCE::Map: Provides a parallel map model similar to the native map function.
MCE::Step: Provides a parallel step implementation utilizing MCE::Queue between user tasks. MCE::Step is a spin off from MCE::Flow with a touch of MCE::Stream. This model, introduced in 1.506, allows one to pass data from one sub-task into the next transparently.
MCE::Stream: Provides an efficient parallel implementation for chaining multiple maps and greps together through user_tasks and MCE::Queue. Like with MCE::Flow, MCE::Stream can run multiple code blocks in parallel with a slight change to syntax from MCE::Map and MCE::Grep.

MISCELLANEOUS

Miscellaneous additions included with the distribution.

MCE::Examples: Describes various demonstrations for MCE including a Monte Carlo simulation.
MCE::Subs: Exports functions mapped directly to MCE methods; e.g. mce_wid. The module allows 3 options; :manager, :worker, and :getter.

REQUIREMENTS

Perl 5.8.0 or later. PDL::IO::Storable is required in scripts running PDL.

SOURCE AND FURTHER READING

The source, cookbook, and examples are hosted at GitHub.

Open Positions in Pasini’s lab

Sat, 04 Feb 2017 08:17:18 -0600

Computational Biologists
Open to PhD-student and Post-doc candidates
We are looking for wet and computational biologists to work on an ERC funded project in our
laboratory located at the Department of Experimental Oncology of the European Institute of
Oncology in Milan (Italy). The project will focus on different aspects of the function of Polycomb
Group proteins and other chromatin modifying activities in relation to their role in regulating cellular
identity in the development of adult tissues.
The candidates will be in charge of computational analysis and data management related to the
project. She/he will directly interact with the wet scientists working in our laboratory while working
embedded in the community of computational biologists present at our institution. The work will
involve the analysis of sequencing data produced with cutting edge technologies to study gene
expression and chromatin environment including data produced on rare cell populations and single
cells. The applicants must have a good knowledge of programming in python/perl/java along with
strong statistical background and performing analysis in R platform. A biological background is
also recommended however it’s not mandatory for application.
Each applicant should submit a full CV (with a detailed description of her/his background,
expertise, achievements and publication records) together with a letter of intent and at least two
contacts for recommendations (for a post-doc position). Competitive salary will be offered based
on the experience of the candidate. Non Italian as well as Italian applicants that have been working
outside Italy (>3yrs.) will have the opportunity to benefit of a full tax deduction for the first three
years of contract.
Applications should be submitted as single PDF to diego.pasini@ieo.it

Lab https://www.ieo.it/en/RESEARCH/People/Researchers/Pasini-Diego/