<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/27323?offset=1190 https://bioinformaticsonline.com/bookmarks/view/38205/sim3c-read-pair-simulation-of-3c-based-sequencing-methodologies-hic-meta3c-dnase-hic Tue, 13 Nov 2018 07:25:38 -0600 https://bioinformaticsonline.com/bookmarks/view/38205/sim3c-read-pair-simulation-of-3c-based-sequencing-methodologies-hic-meta3c-dnase-hic <![CDATA[sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)]]> Required python modules

  • biopython
  • intervaltree
  • numpy
  • scipy
  • tqdm
  • PyYAML

Address of the bookmark: https://github.com/cerebis/sim3C

]]> Jit https://bioinformaticsonline.com/opportunity/view/22235/project-fellow-bioinformatics-at-central-drug-research-institute Mon, 27 Apr 2015 20:15:45 -0500 <![CDATA[Project Fellow Bioinformatics at Central Drug Research Institute]]> Project Fellow (Bioinformatics)
Central Drug Research Institute
Address: Chattar Manzil, M.G.Road, Kaisarbagh
Postal Code: 226001
City: Lucknow
State: Uttar Pradesh
Pay Scale: Rs.16,000/- (fixed) p.m.
Educational Requirements: M.Sc. in Bioinformatics with 55% marks for Gen. & OBC and 50% marks for SC/ST candidates, Physically and Visually handicapped candidates
Experience Requirements: Experience in computer-assisted scientific research in the area of Drug Design including Bio- molecular modeling and simulation studies, Virtual screening, pharmacophore perception, QSAR etc. Familiarity with Linux/Unixbased computer systems and required to participate and contribute to the development and application of computational models for the design and discovery of novel molecules as inhibitors or chemical probes
Details will be available at: http://cdriindia.org/uploaded/advt_no01-2015.pdf

How To Apply: Eligible candidates required to report for the Interview at 9:00 A.M. sharp on 11-05-2015 (For Position Code No. 001 to 009) and 12-05-2015 (For Position Code No. 010 to 016). Candidates reporting after 10:00 A.M will not be allowed to attend the interview. Eligible candidates may appear before the Selection Committee for interview on the date and time mentioned above at CDRI, B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow-226031. Eligible candidates must bring with them duly filled up application form (which can be downloaded from our website www.cdriindia.org), along with Original certificates as well as attested copies of certificates of examinations starting from matriculation, date of birth, caste certificate (in case of SC/ST/OBC) experience certificate, publication, if any and recent passport size photograph etc. Original documents are essential for verification of the particulars quoted by the candidate in the application form and candidate failed to produce original documents at the time of verification, shall not be allowed to attend the interview. Any request for relaxation in this regard shall not be entertained.
Detail of Interview: 11-05-2015
Age Limit: 28 Years

]]> https://bioinformaticsonline.com/bookmarks/view/38762/katuali-is-a-flexible-consensus-pipeline-implemented-in-snakemake-to-basecall-assemble-and-polish-oxford-nanopore-technologies-sequencing-data Tue, 22 Jan 2019 06:26:55 -0600 https://bioinformaticsonline.com/bookmarks/view/38762/katuali-is-a-flexible-consensus-pipeline-implemented-in-snakemake-to-basecall-assemble-and-polish-oxford-nanopore-technologies-sequencing-data <![CDATA[Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data]]>
  • Run a pipeline processing fast5s to a consensus in a single command.
  • Recommended fixed "standard" and "fast" pipelines.
  • Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath.
  • Seemless distribution of tasks over local or distributed compute.
  • Highly configurable.
  • Open source (Mozilla Public License 2.0).

    • Documentation can be found at https://nanoporetech.github.io/katuali/.

    Address of the bookmark: https://github.com/nanoporetech/katuali

    ]]>     Jit     https://bioinformaticsonline.com/opportunity/view/22269/school-of-life-sciences-jawaharlal-nehru-university-vacancy-of-jrf-srf-ra-in-csir-funded-project Wed, 29 Apr 2015 21:26:19 -0500 <![CDATA[School of Life Sciences, Jawaharlal Nehru University vacancy of JRF / SRF / RA in CSIR funded Project]]> School of Life Sciences, Jawaharlal Nehru University has issued notification dated 27.04.2015 to fill the vacancy of JRF / SRF / RA in CSIR funded Projec entitled "Structural and functional characterization of serine biosynthetic pathway enzymes from entamoeba histolytica". It is good chance to get job with IITKGP and brighten your future. Learn eligibility criteria and apply on or before 08.05.2015.

    Employer: Jawaharlal Nehru University
    Address: Dr. S. Gourinath, Principal Investigator, School Of Life Sciences, Jawaharlal Nehru University, New Delhi-110067
    Email: not mentioned / provided for this job post
    URL: http://www.jnu.ac.in/Career/currentjobs.htm
    Phone: 011 2674 2575
    Skills: not mentioned / required for this job post
    Experience: Experience in molecular biology, structural biology and bioinformatics is desired
    Education: M.Sc. in any field of life sciences.
    Job Location: New Delhi, Delhi, India (View Jobs in New Delhi, Jobs in Delhi, Jobs in India)

    Job Description: School of Life Sciences, Jawaharlal Nehru University vacancy of JRF / SRF / RA in CSIR funded Projec

    Name of the Post: JRF / SRF / RA

    Salary: As per rules

    Required Job Profile:

    Candidate must possess M.Sc. in any field of life sciences.

    Desired Job Profile:

    Candidate having NET - CSIR or UGC and experience in molecular biology, structural biology and bioinformatics is desired and experience with publication is preferred.

    How to apply:

    Eligible and interested candidates should need to apply with complete details to the above mentioned address on or before 08.05.2015.

    Refer to http://www.jnu.ac.in/Career/currentjobs.htm

    ]]>         https://bioinformaticsonline.com/opportunity/view/41039/phd-position-in-translational-medicine Sat, 15 Feb 2020 06:07:19 -0600 <![CDATA[PhD position in Translational Medicine]]> https://www.jobvector.de/jobs-stellenangebote/biologie-life-sciences/wissenschaftliche-r-mitarbeiter-in/phd-position-translational-medicine-129981.html?suid=1b510358c7578e8f75cf04a464fc21a404a574ca

    Essential experience / qualifications:
    Master / Diploma in Biology, Biochemistry, Molecular Medicine or similar; solid knowledge of molecular and cell biological techniques; good English knowledge

    Applications:
    Please send your application (including CV, letter of motivation, contact information of two references, and list of publication) by 13.03.2020 at the latest to:

    Universitätsklinikum Erlangen
    Chirurgische Klinik
    Translational Research Center
    Prof. Dr. rer. nat. Michael Stürzl
    Schwabachanlage 12
    91054 Erlangen
    E-Mail: michael.stuerzl@uk-erlangen.de

    ]]>         https://bioinformaticsonline.com/opportunity/view/22287/research-fellows-at-aimscs-hyderabad Wed, 06 May 2015 06:23:33 -0500 <![CDATA[Research Fellows at AIMSCS, Hyderabad]]> C.R.Rao Advanced Institute of Mathematics, Statistics and Computer Science (AIMSCS) - Hyderabad, Andhra Pradesh
    Advertisement No.: 5/2015

    Research Fellows Systems Biology job vacancy in C.R.Rao Advanced Institute of Mathematics, Statistics and Computer Science (AIMSCS)

    JRF : Qualification - M. Sc in Bioinformatics, Systems Biology, M. Sc statistics, or M. Tech in Bioinformatics,

    Pay Scale : Rs. 25,000

    SRF : Qualification- Qualification prescribed for JRF with 2 years of research experience.

    Pay Scale : Rs. 28,000*

    No.of Post: 2

    Desirable: Candidates should have strong background in Computational biology, bioinformatics, statistics and algorithmic development. In addition to that previous experience of working on Linux, bio-informatics, NGS data analysis and Basic knowledge of biology is desirable. Programming on any one of the programming languages (C, C++, perl, python) and statistical framework (e.g. R, matlab, etc.) is highly desirable.

    More at http://www.crraoaimscs.org/jrf_application_form_2015.pdf

    ]]>         https://bioinformaticsonline.com/bookmarks/view/43801/smudgeplot-inference-of-ploidy-and-heterozygosity-structure-using-whole-genome-sequencing-data Fri, 25 Feb 2022 04:42:09 -0600 https://bioinformaticsonline.com/bookmarks/view/43801/smudgeplot-inference-of-ploidy-and-heterozygosity-structure-using-whole-genome-sequencing-data <![CDATA[Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data]]> This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc.

    Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example:

    smudgeexample

    Address of the bookmark: https://github.com/KamilSJaron/smudgeplot

    ]]>     Neel     https://bioinformaticsonline.com/pages/view/22388/perl-one-liner-basics Sun, 24 May 2015 09:28:33 -0500 https://bioinformaticsonline.com/pages/view/22388/perl-one-liner-basics <![CDATA[Perl One liner basics !!]]> Perl has a ton of command line switches (see perldoc perlrun), but I'm just going to cover the ones you'll commonly need to debug code. The most important switch is -e, for execute (or maybe "engage" :) ). The -e switch takes a quoted string of Perl code and executes it. For example:

    $ perl -e 'print "Hello, World!\n"'
    Hello, World!

    It's important that you use single-quotes to quote the code for -e. This usually means you can't use single-quotes within the one liner code. If you're using Windows cmd.exe or PowerShell, you must use double-quotes instead.

    I'm always forgetting what Perl's predefined special variables do, and often test them at the command line with a one liner to see what they contain. For instance do you remember what $^O is?

    $ perl -e 'print "$^O\n"'
    linux

    It's the operating system name. With that cleared up, let's see what else we can do. If you're using a relatively new Perl (5.10.0 or higher) you can use the -E switch instead of -e. This turns on some of Perl's newer features, like say, which prints a string and appends a newline to it. This saves typing and makes the code cleaner:

    $ perl -E 'say "$^O"'
    linux

    Pretty handy! say is a nifty feature that you'll use again and again.

    ]]>     Abhimanyu Singh     https://bioinformaticsonline.com/researchlabs/view/22416/rosenberg-lab Wed, 27 May 2015 17:52:24 -0500 <![CDATA[Rosenberg lab]]> Research. Research in the lab focuses on mathematical, statistical, and computational problems in evolutionary biology and human genetics. Long-term interests of the lab include topics such as:

    Human genetic variation
    Inference of human evolutionary history from genetic markers
    Statistical analysis of population-genetic data
    Mathematical models of gene genealogies
    Theoretical population genetics
    Combinatorics of evolutionary trees
    The relationship between gene trees and species trees
    The role of human evolutionary genetics in the search for genes that contribute to disease-susceptibility
    More at https://web.stanford.edu/group/rosenberglab/index.html

    ]]>         https://bioinformaticsonline.com/opportunity/view/22437/jrf-bioinformatics-icar-national-research-centre-for-orchids-pakyong Thu, 28 May 2015 19:33:19 -0500 <![CDATA[JRF Bioinformatics @ ICAR - National Research Centre for Orchids Pakyong]]> ICAR - National Research Centre for Orchids

    Pakyong

    F.No:NRCO/Admn/DBT /136 /

    Walk-in-Interviews will be held at 737106, Sikkim for the post of 01 (One Project ‘DBT’s Twinning programme for the NE’ titled “Assessment of some fragrant orchids of north-east India for sustainable improvement of community livelihood”, indicated below. The appointment will be on contractual basis and the incumbents shall not have any regular appointment in ICAR.

    ‘DBT’s Twinning programme for the NE’ titled “Assessment of chemical and genetic divergence of some fragrant orchids of north-east India for sustainable improvement of community livelihood”

    Junior Research Fellow (One post)

    Essential Qualification : a. MSc (with NET qualification) / M.Tech degree (with or without NET) with minimum 55% marks in Biotechnology/ Bioinformatics/ Molecular Biology or any other related field.

    Desirable Qualification: Computer Skills (Linux, Perl, Java, MySQL) with experience in advanced molecular Biology techniques

    2nd June 2015

    Advertisement: www.nrcorchids.nic.in/Employments/Vacancy%20-%20JRF.pdf

    ]]>