BOL: Related items

MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction

Abhi — Mon, 08 Apr 2024 06:19:52 -0500

MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard coefficient. Simulation results highlight the superior speed of MIKE compared to existing state-of-the-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast, 303 Zea, 141 Ficus, 67 Oryza, and 43 Saccharum spontaneum samples. MIKE demonstrated accurate performance across varying evolutionary scales, reproductive modes, and ploidy levels, proving itself as a powerful tool for phylogenetic tree construction.

Address of the bookmark: https://github.com/Argonum-Clever2/mike

Faculty at Indian Institute of Science Education and Research Berhampur

Mon, 19 Dec 2016 03:34:26 -0600

Advt. No: IISERBPR/DoFA/2016/2

Advertisement for Faculty Positions

The IISER Berhampur, an Institute of national importance, established through an act of Parliament is an autonomous organization under the Ministry of HRD, Govt. of India, to promote quality education and cutting edge research in basic sciences and to provide a platform for the faculty to engage in high quality education, at undergraduate and postgraduate levels. The Institute invites applications for faculty positions at the level of Assistant Professor (C) /Assistant Professor in the following disciplines:

1. Biological Sciences

2. Chemistry

3. Computer Sciences

4. Mathematics

5. Physics

Only hard copy of application in the prescribed format, via Speed Post should be sent to the Dean, Faculty Affairs, IISER Berhampur, Industrial Training Institute (ITI) Berhampur, Engineering School Road, Berhampur - 760 010, Ganjam District, Odisha, before 1700 hrs., December 30, 2016.

http://www.iiserbpr.ac.in

More Info : http://www.iiserbpr.ac.in/vacancies/Advertisement%20for%20Faculty%20Positions%20at%20IISER%20Berhampur.pdf

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

Postdoc at UBritishColumbia in TroutGenomics

Thu, 22 Dec 2016 08:18:46 -0600

Landscape Genomics Postdoc at UBC A research team at the University of British Columbia’s Department of Zoology and Biodiversity Research Centre is seeking a postdoctoral researcher in landscape genetics of native rainbow trout (Oncorhynchus mykiss).

This project is part of a larger Genome Canada project on genetics and physiology of adaptation to climate change in rainbow trout, and the population genomics component is in the labs of Eric Taylor and Michael Whitlock. The landscape genomics component primarily involves whole genome sequencing approaches to understanding the genomic basis of adaptation to features of habitat, but also to provide insights into phylogeography and the influence of watershed structure on population subdivision in rainbow trout. A PhD in a related field with expertise in basic theory and bioinformatic analysis of population genomics data is required.

The position is available for one year with renewal for up to three additional years. Salary is $55,000 per year plus benefits. To apply, please send a brief cover letter summarizing your qualifications for the position, a CV, and the names, addresses, phone numbers and emails of three references.

Review of applications will begin January 16, 2017. Address application materials to etaylor@zoology.ubc.ca to whom any questions can also be addressed. etaylor@zoology.ubc.ca

Mauve: a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion

Jit — Sat, 24 Dec 2016 09:20:53 -0600

Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research into comparative genomics and the study of genome-wide evolutionary dynamics.

Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the lengths of sequences being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. However, the current algorithm’s compute time (progressiveMauve) scales cubically in the number of genomes to align, making it unsuitable for datasets containing more than 50-100 bacterial genomes.

Address of the bookmark: http://darlinglab.org/mauve/mauve.html

GenomeRing: alignment visualization based on SuperGenome coordinates

Neel — Wed, 18 Jan 2017 10:24:10 -0600

The number of completely sequenced genomes is continuously rising, allowing for comparative analyses of genomic variation. Such analyses are often based on whole-genome alignments to elucidate structural differences arising from insertions, deletions or from rearrangement events. Computational tools that can visualize genome alignments in a meaningful manner are needed to help researchers gain new insights into the underlying data. Such visualizations typically are either realized in a linear fashion as in genome browsers or by using a circular approach, where relationships between genomic regions are indicated by arcs. Both methods allow for the integration of additional information such as experimental data or annotations. However, providing a visualization that still allows for a quick and comprehensive interpretation of all important genomic variations together with various supplemental data, which may be highly heterogeneous, remains a challenge.

More at https://academic.oup.com/bioinformatics/article/28/12/i7/268598/GenomeRing-alignment-visualization-based-on

Address of the bookmark: http://it.informatik.uni-tuebingen.de/?page_id=185

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/

Important Journals, Blogs and Forums for Bioinformaticians

Jit — Wed, 08 Feb 2017 09:15:31 -0600

Journals. Most journals have RSS feeds for their current updates.

Blogs. Some of these blogs are very relevant to bioinfo jobs. Others are more personal interest.

The OpenHelix Blog
Ensembl blog
Galaxy News
Blue Collar Bioinformatics
Homologus
Golden Helix - our 2 SNPs
Genomics Law Report
R-bloggers (aggregates feeds from >350 blogs about R)
Genomes Unzipped
Jason Moore's Epistasis Blog
23andMe - the Spitoon

Variance Explained: David Robinson’s blog (Data Scientist at Stack Overflow, works in R and Python).
Global Biodefense: News on pathogens, outbreaks, and preparedness, with periodic posts on genomics and bioinformatics-related developments and funding opportunities.
In between lines of code: Lex Nederbragt’s blog on biology, sequencing, bioinformatics, …
Simply Statistics: A statistics blog by Rafa Irizarry, Roger Peng, and Jeff Leek.
Bits of DNA: Reviews and commentary on computational biology by Lior Pachter (fair warning: dialogue here can get a bit heated!).
Blue Collar Bioinformatics: articles related tool validation and the open source bioinformatics community.
Microbiome Digest – Bik’s Picks: A daily digest of scientific microbiome papers, by Elisabeth Bik, Science Editor at uBiome.
Living in an Ivory Basement: Titus Brown’s blog on metagenomics, open science, testing, reproducibility, and programming.
Enseqlopedia: James Hadfield’s blog on all things NGS.
Epistasis Blog: Jason Moore’s computational biology blog.
RStudio Blog: announcements about new RStudio functionality, updates about the tidyverse, and more.
nextgenseek.com: Next-Gen Sequencing Blog covering new developments in NGS data & analysis.
RNA-Seq Blog: Transcriptome Research & Industry News.
The Allium: We all need a little humor in our lives. Like The Onion, but for science.

Forums.