Pune University Vacancy Details:
Total No. of Posts: 03
Name of the Post: Project Assistant

Educational Qualification: Candidates should possess M.Sc Degree in Biotechnology/ Biochemistry/ Virology/ Microbiology/ Bioinformatics/ Botany/ Zoology/ Molecular Biology/ Genetics with first class or equivalent GPA with relevant experience.

Selection Process: Shortlisted candidates will be called for interview.

How to Apply: Eligible candidates may send their applications along with detailed biodata with recent passport size photo & self attested copies of relevant documents as mentioned in the notification in an envelope should be superscribed with specialization of subject & cast addressed to UPE Phase II, Focus Area, Biotechnology at Savitribai Phule Pune University on or before 28-02-2015.

Last Date for Receipt of Applications: 28-02-2015.

Read more: Pune University Recruitment 2015 - Project Asst Posts http://www.freejobalert.com/university-of-pune/6941/#ixzz3Sfhtn4hb

http://www.freejobalert.com/wp-content/uploads/2015/01/Notification-Pune-University-Project-Asst-Posts.pdf

FIGENO is a
  FIGure
    GENerator
for GENOmics

With figeno, you can plot various types of sequencing data along genomic coordinates. Video overview: https://www.youtube.com/watch?v=h1cBeXoSYTA.

Address of the bookmark: https://github.com/CompEpigen/figeno

R-language: http://www.r-project.org

BioConductor: http://www.bioconductor.org

Advantages of R

• Free!
• Powerful, many libraries have been created to perform application specific tasks. e.g. analysis of microarray experiments and Next-Gen sequencing (bioconductor: including Bioseq group).
• Presentation quality graphics
  • Save as a png, pdf or svg
• History
  • What you do can be saved for the next time you use R.
  • Ability to turn it into an automated script to perform again and again on different data

Disadvantages

• Lack of a comprehensive graphical user interface, but two do exist: However some do exist: R commander: http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/ and Limma-gui (microarrays) : http://bioinf.wehi.edu.au/limmaGUI/

Preparation

• (Optional) Download and save the tutorial data set from
  • http://bioinformatics.knowledgeblog.org/wp-content/uploads/bioinf/kerr/data.tsv
  • Start R (type R on a Linux or Mac terminal, or find the starting link from PC)

Getting More Help

• Project Home page
  • http://www.r-project.org/
  • Check out the ‘introduction to R’, which is a much more in depth guide .
  • Also R has a built-in help system (see later)

Working directory

This is the directory used to store your data and results. It is useful if it is also the directory where your input data is stored.

• Mac/Linux: this is the directory where you typed in R
• PC: Change using the change working directory option

Common uses of the tool include:

• Displaying the sequence and/or genes in a GenBank flat file.
• Highlighting differences and/or similarities in gene content between related organisms.
• Comparing SNPs and indels between closely-related strains or serovars.
• Comparing gene expression values across multiple samples or timepoints.
• Visualizing coverage plots of RNA-Seq read alignments.

Key Features

Circleator...

• Builds on BioPerl and the input file formats that it supports, including:
  • GenBank flat files, GFF, FASTA
• Accepts a number of other commonly-used datatypes and file formats:
  • BSR and TRF output, SAM/BAM files, VCF-encoded SNPs, tab-delimited files
• Outputs publication-ready figures in the SVG (Scalable Vector Graphics) format.
• Requires only a single configuration file whose layout mirrors that of the figure itself.
  • Predefined configuration files and "track" types are supplied for common datasets.
  • Advanced features allow limited analyses to be performed as a figure is drawn.
• Includes an extensive set of regression tests.
• Offers a prototype web-based GUI (under the "Ringmaster" project.)

https://github.com/jonathancrabtree/Circleator

Address of the bookmark: https://github.com/jonathancrabtree/Circleator

Walk-in-Interview will be held on 04th March 2015 at 11.30 A.M. in the Bio- Informatics Centre of Bose Institute, P-1/12, C.I.T. Scheme VII-M, Kolkata- 700054 for two (02) positions of Research Associate/ Extended Senior Research Fellow in the DBT sponsored following two projects running under the CoE- Bioinformatics under the guidance of Prof. Pinakpani Chakrabarti, Bioinformatics Centre.

Position : RA/SRF
Project title : 1. "Centre of Excellence (CoE) in Bioinformatics at Bose Institute”,2. Project entitled “Setting up of National Facility on Interactive Graphysics Computer System (IGCS) for Biomolecular Modeling, Molecular Dynamics & Structures”

Desired Profile : Ph.D degree in Biological or Chemical Sciences with in-depth understanding of protein structure and dynamics for R.A. position.Those who have submitted thesis can be considered for Extended SRF position
Preferred : Knowledge of computer programming and bioinformatics softwares.
Stipend : For R.A- Rs. 22,000/- p.m., plus admissible H.R.A. and Medical benefit. For Extended SRF - Rs. 20,000/- p.m., plus admissible H.R.A.and Medical benefit.
Age : For R.A- Below 35 years; For Extended SRF - Below 33 years
Interested and eligible candidates should appear before the Selection Committee with atyped application addressed to the Sr.Prof. & In-Charge, Registrar's Office, Bose Institute, P- 1/12, CIT Scheme VII-M, Kankurgachi, Kolkata-700054 along with Bio-data giving details of qualification i.e. examination passed, year, division, percentage of marks from Secondary onwards with attested copies of Certificates, Mark-Sheet and testimonials. The candidates should also bring the original mark-sheets, certificates etc. at the time of Interview.

Walk in Interview : 04.03.15

More at http://www.boseinst.ernet.in/ADVT/14/p_34.pdf

Background

The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degeneration of CHSs.

Address of the bookmark: https://almob.biomedcentral.com/articles/10.1186/1748-7188-4-2

Research Associate Biotechnology /JRF / Lab. Assistant recruitment in Indian Institute of Vegetable Research

Project:
Genomics assisted selection of Solanum chilense introgression lines for enhancing drought tolerance in tomato
Post Name : Research Associate
Qualification : Ph.D in Biotechnology/ Bioinformatics/Genetics & Plant Breeding. M. Tech in Computer Science with at least one research paper in science citation indexed journal. Desirable: Experience in bioinformatics and next generation sequence data handling. Familiarity in Linux, R, Perl/Phython or other programming languages. Willingness to travel to European partner centers.

Pay Scale : Rs. 36000 for 1st and 2nd year as per rules for Research Associate. Rs. 25000/- for 1st and 2nd year and Rs. 28000 as per rules for Junior Research Fellow. Rs. 7000/- for Lab. Assistant.

Age : Not more than 35 years for Men and 40 years for Women (Relaxable for SC/ST/OBC/PH candidates as per rules) for Research Associate/ Junior Research Fellow. Minimum age will be 21 years and maximum age will be 45 years (Relaxable for SC/ST/OBC/PH candidates as per rules) for Lab.Assistant.

More at http://iivr.org.in/Job%20Oppurtunities/RA20.03.2015.pdf

Main features:

1. works with any number of scaffold assemblies in de-novo non-progressive fashion
2. allows to simultaneously work with scaffold assemblies obtained from any in silico and in vitro techniques, supporting multiple existing formats via built-in converters
3. creates an extensive report with several comparative quality metrics (both on assembly level and on the level of individual assembly points)
4. constructs a merged combined scaffold assembly
5. provides an interactive framework for a visual comparative analysis of the given assemblies

Address of the bookmark: https://cblab.org/camsa/

A walk-in-Interview is proposed to be held at National Bureau of Animal Genetic Resources, Karnal (Haryana)-132001 at 10:30 AM on 19.08.2015 to select One Research Associate & Three Senior Research Fellow as per details given below:

Name of the project & project period: ICAR Consortium Platform on Genomics.

The post duration is Upto 31.03.2017 or earlier & Co-terminus with the project.

Upto 31.03.2017 or earlier and Coterminus with the project

Essential Qualifications: PhD degree in Bioinformatics OR Master’s degree in Bioinformatics with 4 years/5 years of Bachelor’s degree having 1st division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from Fellowship/Associateship

Desirable: Working experience in Next Generation Sequencing data analysis

Emolument: Research Associates may be fixed at a consolidated amount at one of the two pay levels given below depending upon the qualification & experience.

I. Research Associate – Master Degree Holders Rs. 38,000/ + HRA II. Research Associate – Doctoral Degree Holder Rs. 40,000/ + HRA

Senior Research Fellow: Two:- Bioinformatics One: - Biotechnology.

Duration of engagement: Upto 31.03.2017 or earlier and Coterminus with the project

Essential Qualifications: Master degree in any one of discipline/ Subjects- Biotechnology/Bioinformatics with 4 years/5 years of Bachelor’s degree.

Candidates having post graduate degree in above mentioned subjects with 3 years Bachelor’s degree should have NET qualification.

Desirable: The candidates should have zeal to work in R environment and NGS data analysis Emolument: Rs. 28,000/- per month + HRA as per admissibility

Age Limit: 1. 40 year for Men and 45 years for Women in case of RA on the date of Interview. 2. 35 year for Men and 40 years for Women in case of SRF on the date of Interview. (Relaxation for SC/ST/OBC and PHC as per GOI/ICAR rules) The above positions are purely temporary and will be filled in on Contractual basis. The selected candidate shall have no right/claim for regular appointment at this Institute, as the engagement is co-terminus with the Project/Scheme.

Interested candidates may attend Walk-in-Interview at 10:30 AM on 19.08.2015 alongwith original certificates and typed bio-data with one set of attested copies of each their certificates with passport size photograph. No TA/DA will be paid for attending the interview. All eligible candidates are advised to be present at least 30 minutes before scheduled time on the date of interview for completing necessary formalities. Canvassing in any form will disqualify the candidates.

More at http://210.212.93.85/Advertisiment3.pdf

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