BOL: Related items

Bioinformatics Faculty at University of Pune

Fri, 13 Nov 2015 03:06:00 -0600

SAVITRIBAI PHULE PUNE UNIVERSITY
(Formerly University of Pune)
(APPOINTMENT OF TEACHING POSTS)

Accompaniment to the Advertisement No. 52 dated 10.11.2015 for various Teaching Positions purely on contract basis for a maximum period of five years in the various Departments/Centre of the University.

Last date for receipt of application in the University Office is 04.12.2015.

Associate Professor

Environmental Science

Institute of Bioinformatics & Biotechnology (IBB)

Microbiology

Assistant Professor

Biotechnology

Institute of Bioinformatics & Biotechnology (IBB)

Microbiology

More Info : http://collegecirculars.unipune.ac.in/sites/documents/Job%20Openings/advt-no-52-dt-10-11-2015-contract-positions.pdf

TAREAN: A computational tool for identification and characterization of satellite DNA from unassembled short reads

Surabhi Chaudhary — Tue, 15 May 2018 02:53:11 -0500

TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.

How to use TAREAN:

Install a local instance of the pipeline using its source code available from bitbucket repository.
Use public Galaxy-based server at https://repeatexplorer-elixir.cerit-sc.cz/. The server is provided in frame of the Elixir CZ project and is maintained by CESNET and CERIT-SC. Simple registration is required to use this service.

Development of TAREAN was supported by ELIXIR CZ research infrastructure project (MEYS Grant No: LM2015047).

References

Novak, P., Avila Robledillo, L., Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) – TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res., doi:10.1093/nar/gkx257

Address of the bookmark: https://bitbucket.org/petrnovak/repex_tarean

Postdoctoral positions are available at the Faryabi Lab

Sun, 11 Oct 2015 03:36:18 -0500

Postdoctoral positions are available at the Faryabi Lab located in the Department of Pathology and the Center for Personalized Diagnostics at the University of Pennsylvania.

A qualified candidate will be strongly motivated individual with following qualifications: a Ph.D. in computational sciences, engineering, physics, bioinformatics, or related field. Ability to program in Python/Perl and R in Unix environment, knowledge of C++, Java, and SQL is a plus. Demonstrated applied bioinformatics/computational proficiency as evidenced by relevant publications in peer-reviewed journals. Experience with cancer genomics is a plus.

The primary research focus of the Faryabi Lab is on developing novel computational methods to study mechanisms involved in genome instability and elucidate their roles in tumorigenesis. In addition the position provides collaborative opportunities with both basic and translational scientists across the Perelman School of Medicine, one of the top 5 medical research universities in the nation.
. a Ph.D. degree in either physical or computational sciences
. solid programming skills ( Python/Perl, Java, C/C++, R, SQL)
. computational genomics experience ( high throughput sequence analysis)
. excellent spoken and written communication and interaction skills
. publications in English in relevant areas of research in peer-reviewed journals.
. Previous experience or interest in data visualization design is a plus.

More at
University of Pennsylvania
Pathology and Laboratory Medicine
Robert B. Faryabi
faryabiPenn@gmail.com
http://faryabib.github.io/
How To Apply: email CV and contacts of 3 references to faryabiPenn@gmail.com

npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads

Shruti Paniwala — Mon, 11 Jun 2018 05:14:57 -0500

npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple structural analyses such as gene ordering, plasmid forming.

Address of the bookmark: http://japsa.readthedocs.io/en/latest/tools/jsa.np.npscarf.html

Research Associates/Research Fellow - School of Agricultural Biotechnology (Last Date 17-11-2015 and Interview on 26-11-2015 at 11.00 AM)

Fri, 13 Nov 2015 02:46:59 -0600

PAU Recruitment November 2015, Punjab

Job notification in Punjab Agricultural University (PAU) for research Associate/ Research Fellow posts for different projects. Eligible candidates may apply in prescribed application format on or before 17-11-2015 from 09:00 am to 05:00 pm.

Vacancies:
Research Associate/ Research Fellow-03
Qualification:
Candidates should possess B.Sc. with minimum 50% marks, M.Sc. in Bioinformatics/ Biotechnology/ Genetics/ Plant Breeding/ Plant Breeding & Genetics/ Plant Breeding, Genetics & Biotechnology/ Microbiology/ Biochemistry/ Botany with 65% marks.
Selection Process:
Selection will be based on interview.
How to Apply:
Eligible candidates may send their applications along with attested copies of certificates, fee to the Director, School of Agricultural Biotechnology, PAU, Ludhiana on or before 17-11-2015 from 09:00 am to 05:00 pm
Last Date:
17-11-2015

More at http://web.pau.edu/content/banner/1349.pdf

SimLoRD: A read simulator for third generation sequencing reads

Aaryan Lokwani — Wed, 22 Aug 2018 10:40:27 -0500

SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model.

Reads are simulated from both strands of a provided or randomly generated reference sequence.

The reference can be read from a FASTA file or randomly generated with a given GC content. It can consist of several chromosomes, whose structure is respected when drawing reads. (Simulation of genome rearrangements may be incorporated at a later stage.)
The read lengths can be determined in four ways: drawing from a log-normal distribution (typical for genomic DNA), sampling from an existing FASTQ file (typical for RNA), sampling from a a text file with integers (RNA), or using a fixed length
Quality values and number of passes depend on fragment length.
Provided subread error probabilities are modified according to number of passes
Outputs reads in FASTQ format and alignments in SAM format

Address of the bookmark: https://bitbucket.org/genomeinformatics/simlord/

JRF Bioinformatics

Mon, 02 Nov 2015 03:24:50 -0600

JRF Bioinformatics

Eligibility : ME/M.Tech, MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech, Microbiology), BE/B.Tech

Location : Gandhinagar

Last Date : 05 Nov 2015

Hiring Process : Face to Face Interview

Junior Research Fellow (JRF) Job vacancies in Gujarat State Biotechnology Mission (GSBTM)

Project : “Establishing a network in computational and system biology”

No. of Post : 01

Qualification : MSc. /M.Tech. /B.E. /B.Tech. in Biotechnology/Bioinformatics /Life Sciences /Microbiology /Biochemistry /Genetics from recognized University. Preference would be given to the candidates having NET/GATE.

Fellowship : Rs. 12,000 + 20% HRA
How to apply

Applications should be filled Online. The last date for submission of application is 5th November, 2015.

More at http://btm.gujarat.gov.in/btm/recruitment2.htm

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

BioStar — Fri, 21 Sep 2018 10:19:52 -0500

Development packages for zlib and libbz2 are needed, as well as a standard compiler environment. On Ubuntu, this can be installed via:

sudo apt-get install build-essential libtool automake zlib1g-dev libbz2-dev pkg-config

On MacOS, the Apple Developer tools and Fink (or MacPorts or Brew) must be installed, then:

sudo fink install bzip2-dev pkgconfig

Address of the bookmark: https://github.com/neufeld/pandaseq

Project Assistant-II job vacancies in National Institute of Oceanography (NIO Goa)

Fri, 06 Nov 2015 01:33:22 -0600

Vacancy no : GAP0423/1509-15

Project Assistant-II job vacancies in National Institute of Oceanography (NIO Goa)

Project Title and Code : Biotechnology Information System. -- GAP0423

Qualification : M.Sc Bioinformatics / Zoology / Botany / Environmental Science. Desirable : Basic understanding of biodiversity concept is desirable

No. of Post : 01

Age : 28 Years

Place of Posting : Goa

Consolidated Stipend Per Month : Rs.16000/-

Job Requirement : Collection and handling of biodiversity data as assigned by the scientists and working with in-house biodiversity data management applications and software
How to apply

Candidates satisfying requirements may attend the Walk-in-interview on 12.11.2015, 10.00 AM at NIO Dona Paula, Goa-403004 along with their bio-data, attested copies of certificates & mark lists in proof of qualification (SSC onwards), age, experience and testimonials. Candidates should bring a photo identity proof at the time of registration

More at http://www.nio.org/index/option/com_vacgoa/task/show/title/Goa/tid/6/sid/28/thid/64

wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly

BioStar — Mon, 04 Feb 2019 04:53:47 -0600

Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output.

./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo prefix
./wtpoa-cns -t 16 -i prefix.ctg.lay.gz -fo prefix.ctg.fa

Address of the bookmark: https://github.com/ruanjue/wtdbg2