BOL: Related items

gbtools: Interactive Visualization of Metagenome Bins in R

Jit — Sun, 26 Mar 2017 15:41:31 -0500

We have developed gbtools, a software package that allows users to visualize metagenomic assemblies by plotting coverage (sequencing depth) and GC values of contigs, and also to annotate the plots with taxonomic information. Different sets of annotations, including taxonomic assignments from conserved marker genes or SSU rRNA genes, can be imported simultaneously; users can choose which annotations to plot. Bins can be manually defined from plots, or be imported from third-party binning tools and overlaid onto plots, such that results from different methods can be compared side-by-side. gbtools reports summary statistics of bins including marker gene completeness, and allows the user to add or subtract bins with each other.

Tool at https://github.com/kbseah/genome-bin-tools

Address of the bookmark: http://journal.frontiersin.org/article/10.3389/fmicb.2015.01451/full

scikit-bio™ is an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics.

Jit — Fri, 02 Mar 2018 04:29:47 -0600

scikit-bio is currently in beta. We are very actively developing it, and backward-incompatible interface changes can and will arise. To avoid these types of changes being a surprise to our users, our public APIs are decorated to make it clear to users when an API can be relied upon (stable) and when it may be subject to change (experimental). See the API stability docs for more details, including what we mean by stable and experimental in this context.

Address of the bookmark: http://scikit-bio.org/

Structural polymorphism analysis from NGS data

Sat, 13 Jul 2013 17:12:47 -0500

The LabEx BASC (Biodiversity, Agroecosystems, Society, Climate), a network of 13 laboratories of the Paris-Saclay Scientific Cluster, is seeking a bioinformatician to analyze Next Generation Sequencing (NGS) data analysis. In the context of a flagship project aiming at understanding and improving the adaptive capacity of agroecosystems it will be critical to establish a link between sequence variation, functional variation, gene/protein expression and phenotypic adaptation.

The successful candidate will be in charge of the detection of polymorphisms including structural variants, of the comparison of multiple and diverse genomes of a same species and of the construction of pan- and core-genomes. These challenging tasks will require bioinformatics developments and implementation of methods for accommodating the high level of repetitiveness of complex genomes. The tools will be integrated into pipelines and made available to end-users through the Galaxy platform. The bioinformatician will therefore also have to provide researchers with advices on their experimental designs in order to ensure compliance of produced datasets with pipelines requirements. He/she will be hosted by a bioinformatics/informatics team (7 people) (http://moulon.inra.fr/index.php/fr/equipestransversales/atelier-de-bioinformatique) which has computational facilities and expertise in NGS data analysis, and will benefit as well from national and international collaborative networks (Aplibio http://www.renabi.fr/platforms/aplibio/, Transplant http://transplantdb.eu, AMAIZING http://www.amaizing.fr/).

The position requires a doctoral degree (PhD) in bioinformatics with strong expertise in script writing (Python/Perl) and pipeline development.

Applicants should send a CV and the names of 2 referees willing to provide a letter of recommendation to joets@moulon.inra.fr.

IBL laboratory

Mon, 12 Aug 2013 02:02:29 -0500

The IBL laboratory focuses on the multi-disciplinary analyses of the global responses of model microorganisms, cyanobacteria (mainly Synechocystis PCC6803) and yeasts (mainly Saccharomyces cerevisae) to environmental stresses triggered by oxidative agents, heavy metals, or drastic changes in nutrients availability. The genome-wide responses studied with the "omics" techniques (transcriptomics, proteomics, metabolomics and genetics) generate a wealth of experimental data, which are processed, archived, integrated and represented as working models through bioinformatics and mathematics.

Link : http://www-dsv.cea.fr/en/instituts/institut-de-biologie-et-de-technologies-de-saclay-ibitec-s/unites-de-recherche/service-de-biologie-integrative-et-genetique-moleculaire-sbigem/laboratoire-de-biologie-integrative-lbi/presentation__1

List of Bioinformatics and Computational Biology Journals

Jitendra Narayan — Wed, 17 Jul 2013 02:36:53 -0500

Hi Bioinformatician and Computational Biologist, this is the comprehensive list of all (?) the bioinformatics and computational biology journals. Please update me if you know any other good journals related with our domains. Feel free to add your comments and suggestions. You comments will be helpful for others...

*The journals are not listed in any ascending, descending, or impact factors oders.

Bioinformatics

Journal of Computational Biology

Briefings in Bioinformatics

Protein Engineering

Nucleic Acids Research

Trends in Biotechnology

Proceedings of the National Academy of Sciences

Folding and Design

Genome Biology

Journal of Biomedical Informatics

Bioinformation

Journal of Computational Intelligence in Bioinformatics

Journal of Structural and Functional Genomics

Journal of Molecular Graphics and Modelling

Metabolic Engineering

Computers & Chemistry

Artificial Intelligence in Medicine

Journal of Biomedical Science

Artificial Intelligence

Machine Learning

Applied Bioinformatics

Applied Genomics and Proteomics

BMC Bioinformatics

Online Journal of Bioinformatics (OJB)

PSB On-Line Proceedings

Bioinformatics: Information Technology & Systems (BITS)

Data Mining and Knowledge Discovery

The EMBO Journal

Current Opinions in Structural Biology

Journal of Molecular Microbiology and Biotechnology

Nature

Nature Structural Biology

Journal of Machine Learning Research

Nature Genetics

Current Opinion in Genetics & Development

Nature Biotechnology

Trends in Biochemical Sciences

Proteins: Structure, Function, and Genetics

Nature Cell Biology

Trends in Genetics

ChemBioChem

Trends in Molecular Medicine

Journal of Molecular Modelling

Trends in Pharmacological Sciences

Drug Discovery Today

Others Free Online Full-text Journals

DIYA: a bacterial annotation pipeline for any genomics lab

Jit — Fri, 30 Jun 2017 08:48:26 -0500

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

http://gmod.org/wiki/Diya

Address of the bookmark: https://sourceforge.net/projects/diyg/

Sr.Bioinformatics Analyst (NGS) at Ocimum

Fri, 17 Nov 2017 07:50:44 -0600

JOB FUNCTIONBio Tech/R&D/Scientist
INDUSTRYBiotechnology/Pharmaceutical/Medicine
SPECIALIZATIONBasic Research,Bio-Statistician,Clinical Research
QUALIFICATION
Any Post Graduate
BA (Arts), B.Com. (Commerce), BE/ B.Tech (Engineering), B.Pharm. (Pharmacy), B.Sc. (Science), BL/LLB, BDS (Dental Surgery), B.Ed. (Education), BHM (Hotel Management), BBA/ BBM/ BBS, B.Arch. (Architecture), BCA (Computer Application), Diploma-Other Diploma, B.Plan. (Planning), BGL, B.V.Sc. (Veterinary Science), Other School/ Graduation, BHMS (Homeopathy), BAMS (Ayurveda)
Job Description

1. Must have basic understanding of molecular biology and Genomics.
2. Experience in application development or must have expertise in programming using either of Perl/Python.
3. Experience in statistical programming using R/Bioconductor/Matlab.
4. Strong concept in statistical and mathematical modelling.
5. Experience in designing and developing the bioinformatics pipeline.
6. Must have minimum 2+ years of hands on experience in NSG data analysis such as RNA-Seq,Exome-Seq ,Chip-Seq and downstream analysis.
7. Knowledge in WGS ,WES, Targeted re-sequencing,GWAS and population genomics will be preferred.
8. Must have experience working on opensource software/Framework and commercial software for NGS data analysis and reporting.
9. Should be aware of handling big data and guiding team members on multiple projects simultaneously.
10. Should have experience coordinating with different groups of clinical research scientist for various project requirements.
11. Ability to work as team as well as independently with minimal support.

More at http://www3.ocimumbio.com/

BioPython Cookbook

Jitendra Narayan — Thu, 08 Aug 2013 06:43:02 -0500

If you are planning to start learning BioPython ( it does not bite but swallow :P just kidding) then this online cookbook will be really helpful for you.

http://biopython.org/DIST/docs/tutorial/Tutorial.html

List of pharmacogenomics companies worldwide

Jitendra Narayan — Fri, 09 Aug 2013 13:24:47 -0500

Pharmacogenomics are the most promising area of research. Here is the list of some Pharmacogenomics companies worldwide. Feel free to add more pharmacogenomics companies if not mentioned in here.

Great Pharmacogenomics companies
www.aruplab.com
www.clarientinc.com
www.cns-hts.com
www.dnanow.com
www.dnavision.be
www.dnavision.com
www.dxsdiagnostics.com
www.entrogen.com
www.exiqon.com
www.gene.com
www.genomichealth.com
www.genoptix.com
www.genpathdiagnostics.com
www.gentris.com
www.immunicon.com
www.ingenuity.com
www.lab21.com
www.labcorp.com
www.lion-ag.de
www.lynxgen.com
www.mayoclinic.com
www.mesoscale.com
www.microcide.com
www.mitokor.com
www.monarchlifesciences.com
www.mplnet.com
www.orchidbio.com
www.pebio.com
www.phenomenome.com
www.phenopath.com
www.ppgx.com
www.prometheuslabs.com
www.protogene.com
www.questdiagnostics.com
www.rigelinc.com
www.rii.com
www.saladax.com
www.tmdlab.com
www.transgenomic.com
www.twt.com
www.uslabs.net
www.variagenics.com

Great Equipment Companies for Genomics
www.affymetrix.com
www.illumina.com
www.iontorrent.com
www.sequenom.com
www.appliedbiosystems.com
www.454.com
www.appliedbiosystems.com

Genomics in India
www.ganitlabs.in
www.sandor.co.in
www.igib.res.in
www.genotypic.co.in
www.ocimumbio.com
www.abcgenomics.com
www.xcelrisgenomics.com
www.ayugen.com
www.geneombiotech.com

Large Global Whole Genome Companies
www.decode.com
www.23andme.com
www.navigenics.com
www.pathway.com

Global companies offering genomics services
www.asuragen.com
www.baseclear.com
www.agtcenter.com
www.ambrygen.com
www.arosab.com
www.agrf.org.au
www.beckmangenomics.com
www.genomics.cn
www.bsf.a-star.edu.sg
www.cbm.fvg.it
www.cincinnatichildrens.org
www.cofactorgenomics.com
www.covance.com
www.dnalandmarks.ca
www.dnavision.com
www.expressionanalysis.com
www.fasteris.com
www.gatc-biotech.com
www.genesdiffusion.com
www.geneseek.com
www.geneticvisions.com
www.geneworks.com.au
www.genizon.com
www.genoskan.dk/uk
www.gpbio.jp
www.igatechnology.com
www.igenixinc.com
www.auxologico.it
www.lifeandbrain.com
www.macrogen.co.kr/eng
www.gqinnovationcenter.com
www.mftservices.de
www.ncgr.org
www.ramaciotti.unsw.edu.au
www.rikengenesis.jp
www.SABiosciences.com
www.sequensysbio.com
www.servicexs.com
www.snp-genetics.com
www.takara-bio.com
www.gen-probe.com
www.traitgenetics.com

Bioinformatics Services / CRO Services

RASA Life Sciences — Wed, 06 Nov 2019 00:33:11 -0600

RASA is set to provide premium technical and scientific services in a form of solutions, product development and training. .We are also very proficient in providing the high quality Research & Development services in life science informatics field like Next Generation Sequencing (NGS) Data Analysis,Computational Drug Discovery, Bioinformatics, Chemo-informatics and BIO-IT.

RASA offers faster, better and cost effective cutting edge technology solutions to chemical and life science research and industry. We provide our customers with A seamless model of wide expertise and comprehensive platforms. Our Value is to take our customers