BOL: Related items

OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation

Jit — Tue, 14 Nov 2017 09:30:35 -0600

Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. In closely-related species, gene neighborhood information can be used to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a software for accurately predicting pairwise orthology relations based on gene neighborhood conservation. Analyses on simulated and real data reveal the high accuracy of OrthoGNC. In addition to orthology detection, OrthoGNC can be employed to investigate the conservation of genomic context among potential orthologs detected by other methods. OrthoGNC is freely available online at http://bs.ipm.ir/softwares/orthognc and http://tinyurl.com/orthoGNC.

http://www.comp.nus.edu.sg/~wongls/projects/orthoGNC/

Address of the bookmark: http://www.sciencedirect.com/science/article/pii/S1672022917301663

Bioinformatician’s Pocket Reference !!

RAJESH DETROJA — Sun, 08 Jun 2014 09:56:58 -0500

It is amusing how brain of bioinformaticians work! Learning a new programming language for days feels so much of fun that making 5 minute discussion with neighbours (unless under special circumstances!) in our own mother-tongue. Today every bioinformatician keeps more than few languages and core IT toolkits on their plate. It has become mandatory to be able to mould different code snippets to build our own custom workflows, and thus keeping syntax at our fingertips has become essential.Although Google is best way to get syntax problem solved, it is not a bad idea to keep reference sheets is our smartphones or stick out some printed sheets on the back of your door, in the old fashion way!!

Address of the bookmark: http://infoplatter.wordpress.com/2014/04/06/bioinformaticians-pocket-reference/

Assistant Professor in Medical Bioinformatics

Tue, 24 Jun 2014 01:46:36 -0500

Advt. No : ME-I/A-IV/03/14
No.of Posts:01 (SC)
Pay Scale:
Pay Band of Rs.15600-39100 + Rs.6000/- GP +NPA @ 25% of Basic Pay +Learning Resource Allowance @ Rs.20,000/-P.A.+ Conveyance Allowance @ Rs. 1650/-P.M.+ Academic Allowance @ Rs.2500/- P.M. and other admissible allowances.
Qualifications:
Area of Specialization:-
Bioinformatics/Computational/Biology/Genomics/ Proteomics/ Structural Biology
1. Postgraduate qualification, e.g. Master’s Degree in Biotechnology/Bioinformatics/ Biophysics.
2. A Doctorate Degree of recognized University/Institute in a basic or allied Medical Science subject e.g. Medical Biotechnology/Biophysics. Bioinformatics/X-ray Crystallography/
Immunology/Structural Biology etc
Experience:
1.Minimum three years teaching and/or research experience in a recognized medical/research Institution in an allied medical subject after obtaining doctorate degree and preferably in Medical
Molecular Biology/ Biophysics/Structural Biology/Genomics and Clinical Proteomics/Computational Biology.
2. Minimum two publication with atleast one in international journal and atleast one as first author
Desirable:-
Consistently excellent scholastic/academic record, demonstrated ability to write grant proposal/(s) successfully, Post Doctoral training in a frontier area of medical Bioinformatics Research and of direct relevance to clinical diagnosis or patient care (preferably from a recognized top-ranking medical institution abroad)
Send your applications to O/O, Deputy Registrar, Recruitment & Establishment Cell, University of Health Sciences, Rohtak by 08.7.2014
For more details,please visit website: http://pgimsrohtak.nic.in/2014%20AP%20Advt.pdf
Last Apply Date: 08 Jul 2014

GRIDSS: the Genomic Rearrangement IDentification Software Suite

Rahul Nayak — Sun, 17 May 2020 10:27:44 -0500

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.

Address of the bookmark: https://github.com/PapenfussLab/gridss

Postdoc position at Centre Méditerranéen de Médecine Moléculaire

Sun, 06 Jul 2014 11:23:06 -0500

The research group of Dr. Michele Trabucchi at the Centre Méditerranéen de Médecine Moléculaire (C3M) at INSERM U1065 (University of Nice Sophia-Antipolis, France) is seeking candidates for a Postdoctoral fellow position to start on October 2014 for 3 years funded by FRM (Fondation pour la Recherche Médicale).
The broad interest of the lab is in understanding the expression control and function of small RNAs in activated myeloid cells (visit our webpage to check research interests and publications of the group : http://www.unice.fr/c3m/EN/Equipe10.html ).

The work will focus on the functional studies of small RNAs by using next-generation sequencing approaches.

Candidates should hold a Ph.D. degree and have strong background in bioinformatics.
The University of Nice Sophia-Antipolis provides a wide range of facilities and training essential for biomedical research.
Interested applicants should send a PDF with a cover letter stating research interests and qualifications, an updated CV, a summary of previous research experience and contact information for two references to Michele Trabucchi ( mtrabucchi@unice.fr )

Awesome perl frameworks, libraries and software - PART 5

Neel — Fri, 07 Jul 2017 04:12:47 -0500

robelix/sub2srt - subtitle converter
reyjrar/graphite-scripts - A Collections of Scripts for Working with Graphite
regilero/check_nginx_status - Nagios check for nginx status report
omniti-labs/resmon - resmon
motemen/App-htmlcat - redirect stdin to web browser
moose/Moo - Minimalist Object Orientation (with Moose compatibility)
miyagawa/fastpass - Tiny, XS free, standalone and preforking FastCGI daemon for PSGI
miyagawa/Filesys-Notify-Simple - Simple and dumb file system watcher
mhop/fhem-mirror - Branch 'master' is a read-only-mirror of svn://svn.code.sf.net/p/fhem/code which is updated once a day. On branch 'enocean' I am going to add some Enocean-Devices
lopnor/Plack-App-DAV - simple DAV server for Plack
kazuho/url_compress - a static PPM-based URL compressor / decompressor
jnthn/6model - Just a place that I'm keeping some meta-model prototyping; anything that matters will make it to another repo (e.g. nqp-rx one or Rakudo one) at some point.
jasonhancock/nagios-puppetdb - Nagios plugins and pnp4nagios templates related to Puppetlab's PuppetDB project.
goccy/p5-Compiler-Parser - Create Abstract Syntax Tree for Perl5
cgutteridge/Grinder - Create RDF data from spreadsheets or CSV
c9s/Plack-Middleware-OAuth - Plack Middleware for OAuth1 and OAuth2
bzip2-cuda/bzip2-cuda - Parallel implementation of bzip2 using cuda
alanstevens/ChocoPackages - Chocolatey Nuget Packages
SoylentNews/slashcode - The slashcode repository for SoylentNews. The initial code base was uploaded as it appeared on Sourceforge as of the last commit in September 2009
Miserlou/XSS-Harvest - XSS Weaponization

Nuclear Dynamics Lab

Thu, 17 Jul 2014 15:03:27 -0500

Lab focus is to elucidate fundamental principles, new mechanisms, machineries and emergent properties that are involved in maintaining the genome and gene expression programmes for improvements in lifelong health and well-being for all.

More at http://www.babraham.ac.uk/our-research/nuclear-dynamics/

GenomeTools: The versatile open source genome analysis software

Jit — Wed, 07 Feb 2018 10:44:18 -0600

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.

If you are interested in gene prediction, have a look at GenomeThreader.

Address of the bookmark: http://genometools.org/

Pimp your brain: Bioinformatics

Wed, 20 Aug 2014 22:09:21 -0500

Jan Lisec from the Max Planck Institute of Molecular Plant Physiology explains, in this "pimp your brain" episode, what bioinformatics is and why bioinformatics is so important and indispensable for biological research. In the video serial "Pimp your brain" scientists from the Max Planck Institute of Molecular Plant Physiology describe their research. More videos from the 'Pimp your brain' serial are available on www.youtube.com/playlist?list=PL-l9VItC9Gn2Ur2Xj6PTOAkjLUlVPbIOO More videos are available on www.mpimp-golm.mpg.de

DECIPHER; a software toolset for deciphering and managing biological sequences efficiently using the R

BioStar — Sun, 09 Dec 2018 19:06:17 -0600

DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the R programming language. The R package is distributed as platform independent source code under the GPL version 3 license. Some functionality of the program is accessible online through web tools.

Address of the bookmark: http://www2.decipher.codes/