BOL: Related items

CSBB-v1.0

Neel — Wed, 29 Jun 2016 07:33:05 -0500

CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R and python in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX, MAC OS and Windows platforms.

Currently CSBB provides 13 modules focused on analytical tasks like performing upper-quantile normalization on expression data or convert genome wide gene expression to z-scores when comparing expression data from different platforms.

More at https://github.com/skygenomics/CSBB-v1.0

Address of the bookmark: https://github.com/skygenomics/CSBB-v1.0

Python vs Perl

Rahul Agarwal — Thu, 11 Jul 2013 14:39:19 -0500

Why bioinformatician still using Perl when Python is easy to code, good in ReXp and faster than perl?

Bioinformatics Head (Bioinformatics Manager III), Cancer Genomics Research Laboratory at Frederick National Laboratory

Wed, 18 Aug 2021 00:19:48 -0500

Frederick National Laboratory seeking an enthusiastic, creative, and seasoned bioinformatics professional to join our leadership team and direct the exceptional Bioinformatics Group at the Cancer Genomics Research Laboratory (CGR). CGR has a diverse team of bioinformatics and computational scientists that support all areas of bioinformatics and data analysis (infrastructure, data QC, pipeline development and maintenance, data curation and sharing, methodology development, statistical analyses, machine learning approaches, and scientific interpretation).

More at https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leidosbiomed&id=2040

The Raku Programming Language

Jit — Tue, 28 Jan 2020 05:37:17 -0600

Raku is a member of the Perl family of programming languages. Formerly known as Perl 6, it was renamed in October 2019. Raku introduces elements of many modern and historical languages. Compatibility with Perl was not a goal, though a compatibility mode is part of the specification.

More at https://www.raku.org/

Address of the bookmark: https://www.raku.org/

Which of the following programming language is best for a bioinformatics beginner?

Manisha Mishra — Thu, 04 Sep 2014 07:51:16 -0500

I will be doing NGS in the course of my research work and I will like to learn a programming language which is compatible with most bioinformatics tools or software. I basically want to do de-novo assembly, map reads, align reads, and expression analysis. Recommendations welcomed. Which languages would you recommend to a student wishing to enter the world of bioinformatics?

irishgrid: Irish Grid Mapping System

Jit — Fri, 26 Dec 2014 07:53:24 -0600

Perl module for creating geographic 10km-square maps using either SVG or PNG (with GD library) output format.

Originally design to map the location of objects in a 10 km map IrishGrid includes:

native support of the Irish Grid System (see http://www.osi.ie/)
optimize for speed (there's as less as possible data to conversion)
customized color functions

https://code.google.com/p/irishgrid/downloads/detail?name=irishgrid.pl

Address of the bookmark: https://code.google.com/p/irishgrid/

Reverse Complement Problem Solved with Perl

Jit — Tue, 09 Jun 2015 23:37:23 -0500

Question at http://rosalind.info/problems/1b/

#Find the reverse complement of a DNA string.
#Given: A DNA string Pattern.
#Return: Pattern, the reverse complement of Pattern.

use strict;
use warnings;

my $string="AAAACCCGGT";
my $finalString="";
my %hash = (
   "C" => "G",
   "A" => "T",
   "T" => "A",
   "G" => "C",
);

for (my $aa=0; $aa<=(length($string)-1); $aa++) {
   my $char=substr $string, $aa, 1;
   #print $hash{$char};
   $finalString="$hash{$char}"."$finalString";
}

print $finalString;
print "\n";

SRF/JRF Bioinformatics at CIARI

Fri, 04 Dec 2015 00:10:09 -0600

Realizing the importance of Island Agriculture to meet the requirements of local population and tourists, Indian Council of Agricultural research (ICAR) established Central Island Agricultural Research Institute, Port Blair on June 23rd, 1978 by merging different regional research stations of ICAR institutes located in Islands. The ultimate aim of CIARI is the developments of island agricultural production technologies which utilizes the strengths of the island and convert the constraints in opportunities, without causing any ill effect to the fragile ecosystem of the island.The institute has made tremendous progress in the Agriculture development of the islands during the last three decades. Keeping in view the natural resources of the islands diversity, fragile ecosystem, research program would be designed to maximize the productivity without disturbing to the islands ecosystem to provide better and decent livelihood and as a source of revenue and resource generation. Research and development in Agriculture sector should cover all disciplines in order to have a balanced progress in all disciplines for the overall benefits of the farmers of these islands.

Position I

Job Title : Junior Research Fellow

No. of Posts : One

Project : Establishment of sub distributed information centre

Qualification : M.Sc in Basic Science with NET or B.Sc in professional course with NET or M.Sc in professional course

Desired Experience : Experience in Bioinformatics and molecular biology

Payscale : Rs. 25000 per month

Age Limit : Upto 35 for men and 40 for women with 5 years relaxation to SC/ST and 3 years relaxation for OBC.

Position II

Job Title : Traineeship

No. of Posts : One

Project : Establishment of sub distributed information centre

Qualification : B.Sc Bioinformatics /Biotechnology / Life Science / Computer Science

Desired Experience : Experience in Bioinformatics and molecular biology

Payscale : Rs. 8000 per month

Age Limit : Upto 35 for men and 40 for women with 5 years relaxation to SC/ST and 3 years relaxation for OBC.

Position III

Job Title : Studentship

No. of Posts : Two

Project : Establishment of sub distributed information centre

Qualification : B.Sc Bioinformatics /Biotechnology / Life Science / Computer Science

Desired Experience : Experience in Bioinformatics and molecular biology

Payscale : Rs. 8000 per month

Age Limit : Upto 35 for men and 40 for women with 5 years relaxation to SC/ST and 3 years relaxation for OBC.

How to Apply : Candidates who meet the requirements can attend the walk in interview at CIARI,Port Blair on 09.12.2015 10.30AM.

http://icar-ciari.res.in/employment/9-12-15.pdf

Post-doc position at LABGeM - Evry, France

Fri, 11 Dec 2015 06:24:00 -0600

The LABGeM team (CEA/Genoscope, CNRS UMR 8030, France, Dir. Claudine Médigue) is developing integrated approaches which combines bioinformatics methods based (i) on genomic and metabolic contexts, (ii) on an orignal metabolic network representation and (iii) on a structural classification of active sites for the discovery of new metabolic enzymatic activities.

We are hiring a post-doctoral fellow for the development of innovative bioinformatics methods to explore metabolic networks and enzyme families. These methods will be based on protein family analysis and graph approaches combining genomic and metabolic contexts.

For more details, please see this link : http://goo.gl/tHQOqk

Qualifications:
PhD degree in bioinformatics or computational biology
- Previous experience in network or protein family analysis
- Programming skills (C/C++, Python, Java) and in common biostatistical analyses
- Team player, innovative and creative thinking, good oral and written communication skills

24 months, Post Doctoral position
Start: from March 2016
Place: CEA, Genoscope UMR8030, LABGeM (Laboratory of Bioinformatics Analyses for Genomics and Metabolism), Evry, France
Contact: David Vallenet, vallenet@genoscope.cns.fr
Publications: https://scholar.google.com/citations?user=rJNPLSAAAAAJ
Remuneration per month: from 2,850 €

Interested candidates should send their CV, statement of research interests, and contact information of at least 2 references to David Vallenet (vallenet@genoscope.cns.fr).

Microscope

Jitendra Narayan — Fri, 04 Mar 2016 05:26:31 -0600

Microscope Platform user documentation.

The MicroScope platform is available at this URL:

https://www.genoscope.cns.fr/agc/microscope

Address of the bookmark: http://microscope.readthedocs.org/en/latest/index.html