<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37636?offset=460 https://bioinformaticsonline.com/blog/view/43084/frequently-used-bioinformatics-tools-for-viral-genome-analysis Wed, 23 Jun 2021 07:40:41 -0500 https://bioinformaticsonline.com/blog/view/43084/frequently-used-bioinformatics-tools-for-viral-genome-analysis <![CDATA[Frequently used bioinformatics tools for viral genome analysis !]]> IVA: accurate de novo assembly of RNA virus genomes.
Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD.
Bioinformatics. 2015 Jul 15;31(14):2374-6. doi: 10.1093/bioinformatics/btv120. Epub 2015 Feb 28.

Adapter sequences:
Optimal enzymes for amplifying sequencing libraries.
Quail, M. a et al. Nat. Methods 9, 10-1 (2012).

GAGE:
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Salzberg, S. L. et al. Genome Res. 22, 557-67 (2012).

KMC:
Disk-based k-mer counting on a PC.
Deorowicz, S., Debudaj-Grabysz, A. & Grabowski, S. BMC Bioinformatics 14, 160 (2013).

Kraken:
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood, D. E. & Salzberg, S. L. Genome Biol. 15, R46 (2014).

MUMmer:
Versatile and open software for comparing large genomes.
Kurtz, S. et al. Genome Biol. 5, R12 (2004).

R:
R: A language and environment for statistical computing.
R Core Team (2013). R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.

RATT:
RATT: Rapid Annotation Transfer Tool.
Otto, T. D., Dillon, G. P., Degrave, W. S. & Berriman, M. Nucleic Acids Res. 39, e57 (2011).

SAMtools:
The Sequence Alignment/Map format and SAMtools.
Li, H. et al. Bioinformatics 25, 2078-9 (2009).

Trimmomatic:
Trimmomatic: A flexible trimmer for Illumina Sequence Data.
Bolger, A. M., Lohse, M. & Usadel, B. Bioinformatics 1-7 (2014).

]]> Neel https://bioinformaticsonline.com/opportunity/view/10124/jrf-at-bose-institute-kolkata Mon, 21 Apr 2014 19:41:14 -0500 <![CDATA[JRF at Bose Institute, Kolkata]]> ADVT. No. S/BIC/01/2014-15

Bose Institute, Kolkata, invites applications from Indian Citizens for ONE (01) temporary position of Junior Research Fellow in the DBT sponsored project entitled, “Centre of Excellance (CoE) in Bioinformatics at Bose Institute”, running under Prof. Pinakpani Chakrabarti, Project Co-ordinatior, Bioinformatics Centre. The project is tenable upto 31.03.2017, but duration of the fellowship is one year only. The JRF will work with one of the faculty members of the center based on his / her motivation in any specific area on Bioinformatics.

Essential Qualification: 1st class M.Sc. / M.Tech degree in any stream of Chemical/ Biological Sciences with CSIR-UGC-NET-JRF / ICMR-JRF / DBT-JRF or CSIR-UGCNET- LS / GATE qualification.

Desirable qualification:

(i) Specialized knowledge in Organic / Physical chemistry.
(ii) Any exposure to research involving the small molecules (like drug) and / or protein structure determination or prediction.
(iii) Basic knowledge in computer programming, e.g. using FORTRAN, C, shell, perl etc.
(iv) Hands-on-experience on any of the following software : CHARMM/AMBER/NAMD/GROMACS,Gaussian/Gamess, Haddock/Autodock, Schrodinger etc. (or any other software serving similar purposes in molecular modeling)

Fellowship :

(i) Rs. 16,000/- p.m., plus admissible HRA & Medical Benefit for M.Sc. with CSIRUGC NET-JRF/ICMR-JRF/DBT-JRF or M.Tech. with CSIR-UGC NETJRF/
ICMR-JRF/DBT-JRF/CSIR-UGC NET-LS/GATE
(ii) Rs. 12,000/- p.m., plus admissible HRA & Medical Benefit for M.Sc. with CSIRUGC NET-LS/GATE

Age : Below 28 years as on the day on which the application is made (relaxable in case of SC/ST/OBC/WOMEN candidates only as per rule).

Interested and eligible candidates should apply on plain paper duly signed by them clearly mentioning the area of interest in research, possession of any desirable qualification (s) as mentioned above and quoting Advertisement No. on the envelop as well as application with complete Bio-data giving e-mail ID, Phone No. and details of qualification i.e. examination passed, year, division, percentage of marks, from Secondary onwards with attested copies of testimonials, addressed to the Registrar, Bose Institute, P-1/12, CIT Scheme VII-M, Kankurgachi, Kolkata-700054 on or before April 25, 2014.

The shortlisted candidates will be called for an interview. Applicants are advised to check our website for future updates.

Advertisement: www.boseinst.ernet.in/ADVT/14/p_2.pdf

]]> https://bioinformaticsonline.com/opportunity/view/43329/postdoc-position-at-kiel-university-germany Sat, 28 Aug 2021 01:16:55 -0500 <![CDATA[Postdoc position at Kiel University, Germany]]> In the Genomic Microbiology Group of Prof. Tal Dagan at the Institute
of Microbiology at Kiel University, Germany, a

Postdoc position (m/w/d)

in the field of computational evolutionary microbiology is available
for an initially limited period of 36 months at the earliest possible
date. The weekly working time corresponds to 100% of full employment
(If the legal requirements under collective bargaining law are met, the
tariff grouping is carried out up to pay scale 13 TV-L. The obligation
to teach amounts to 4 hours.

The Genomic Microbiology Group research interests are focused on
microbial genome evolution with an emphasis on the study of lateral gene
transfer. In our research we use both computational and experimental
approaches (see www.uni-kiel.de/genomik). The position offers the
opportunity to develop an independent research profile within the group
research focus. The successful applicant is expected to be involved
in teaching of bioinformatics and molecular evolution, including the
development of teaching materials (lectures/exercises/short videos).

Your profile:
· Doctoral or PhD degree in Molecular Evolution, Bioinformatics or
related fields.
· Knowledge and experience in programming (e.g., Python) and
biostatistical analysis (e.g., with R or MatLab).
· Any of the following expertise is an advantage: the analysis of
genomic or transcriptomic data, phylogenetic reconstruction,
comparative genomics.
· Good oral and written communication skills in English.
· Ability to teach in German is an advantage (alternatively, an
indication to do so from the 2nd year on).
· Skills and motivation to communicate and interact with other
scientists.

The Christian-Albrechts-University sees itself as a modern and
cosmopolitan employer. We welcome your application regardless of your age,
gender, cultural and social background, religion, ideology, disability
or sexual identity. We promote equality of the sexes.

The Christian-Albrechts-University is committed to the employment of
people with disabilities. Preference will be given to applications from
severely handicapped persons and persons of equal standing, provided
they are suitable.

We expressly welcome applications from people with a migration background.

For enquiries regarding the position, teaching obligations and research
topic please contact Prof. Tal Dagan: tdagan@ifam.uni-kiel.de.

Applications should be submitted by email to Mrs. Haacks
(dhaacks@ifam.uni-kiel.de) as a single PDF and include: (1) a letter of
motivation (max 1 page, Arial 11, line spacing 1.15), (2) CV, (3) PhD
certificate. Please use 'GMG postdoc application - [your name]'
as a subject.

Please, refrain from sending us application photos.

Application deadline: August 31 2021 or until the position is
filled. Interviews will take place during September/October 2021. The
planned starting date for the position is flexible (but in 2021).

]]> https://bioinformaticsonline.com/opportunity/view/10262/research-fellow-phd-candidate-in-computational-biology-%E2%80%93-2-positions Fri, 25 Apr 2014 20:19:58 -0500 <![CDATA[Research fellow (PhD candidate) in computational biology – 2 positions]]> At the Department of Informatics two 4-year positions as research fellow are available in the field of computational biology connected to the Computational Biology Unit. The positions are linked to the project “Integrated genomics - linking transcriptional and translational regulation over developmental time” supported by the Bergen Research Foundation

The fate of a cell is ultimately the product of the regulation of its genes. Gene regulation is a coordinated process acting at multiple levels of which transcription and translation are the most prominent. The Valen group is dedicated to the fundamental question of how transcription and translation is integrated to obtain the desired protein abundance. The recent development of high-throughput next generation sequencing techniques to monitor both active translation and transcription has made it possible to study this connection at the genome scale.

This project aims to elucidate the links between regulation of translation and transcription. The applicant will analyze next generation sequencing data and model gene regulation on a genome-wide level to identify the features that affect the translational output of transcripts. The work will be done in close collaboration with experimental scientists who will test the predictions of the computational models.

Additional information on the position can be obtained by contacting Eivind Valen (eivind.valen@ii.uib.no).

The research fellow must take part in the University’s approved PhD program leading to the degree within a time limit of 3 years. Application for admission to the PhD program, including a project plan outline for the training module, will be worked out in collaboration with the research group in question.

In total, the fellowship period is 4 years, 25 % of this will be allocated to teaching and/or administrative duties. The fellowship period may be reduced if the successful applicant has held previous employment as a research fellow or similar.

http://www.jobbnorge.no/en/available-jobs/job/102235/research-fellow-phd-candidate-in-computational-biology-2-positions

]]> https://bioinformaticsonline.com/bookmarks/view/44472/pipesnake-bioinformatics-best-practice-analysis-pipeline-for-phylogenomic-reconstruction Wed, 21 Feb 2024 06:19:41 -0600 https://bioinformaticsonline.com/bookmarks/view/44472/pipesnake-bioinformatics-best-practice-analysis-pipeline-for-phylogenomic-reconstruction <![CDATA[pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction]]> ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

Address of the bookmark: https://github.com/AusARG/pipesnake

]]> LEGE https://bioinformaticsonline.com/opportunity/view/10457/assistant-professor-bio-informatics-at-health-and-family-welfare-department-medical-education-in-raipur Wed, 07 May 2014 00:08:38 -0500 <![CDATA[Assistant Professor (Bio-Informatics) at Health and Family Welfare Department (Medical Education) in Raipur]]> Advertisement No.05/2014/ Exam/Dated 17/04/2014

No of vacancies: 01

Pay scale:Rs. 15600 – 39100 + 6600/-

Essential Academic Qualifications / Experience : Good academic record as defined by the concerned university with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed) at the Master's Degree level in a relevant subject from an Indian University, or an equivalent degree from an accredited foreign university.

Besides fulfilling the above qualifications, the candidate must have cleared the National Eligibility Test (NET) conducted by the UGC, CSIR or similar test accredited by the UGC like SLET/ SET.

Notwithstanding anything contained in sub-clauses (a) and (b) to this Clause, candidates, who are, or have been awarded a Ph.D. Degree in accordance with the University Grants Commission (Minimum Standards and Procedure for Award of Ph.D. Degree) Regulations, 2009, shall be exempted from the requirement of the minimum eligibility condition of NET/SLET/SET for recruitment and appointment of Assistant Professor or equivalent positions in Universities/Colleges/Institutions.

NET/SLET/SET shall also not be required for such Masters Programmes in disciplines for which NET/SLET/SET is not conducted.

Apply online: http://www.psc.cg.gov.in/htm/OA_ME2014.html

Last Date for Online Registration: 22/05/2014

For more details: http://www.psc.cg.gov.in/pdf/Advertisement/ADV_ME2014.pdf

]]> https://bioinformaticsonline.com/pages/view/18749/list-of-biotechnology-research-laboratory-university-and-centre-in-india Thu, 30 Oct 2014 12:34:34 -0500 https://bioinformaticsonline.com/pages/view/18749/list-of-biotechnology-research-laboratory-university-and-centre-in-india <![CDATA[List of Biotechnology Research Laboratory, University, and Centre in India]]> DEPARTMENT OF BIOTECHNOLOGY

INDIAN COUNCIL OF MEDICAL RESEARCH (ICMR)

COUNCIL OF SCIENTIFIC & INDUSTRIAL RESEARCH (CSIR)

 

CITYWISE

City Wise Llist of Govt. and Non Govt. Research institutions in India -

Ahmedabad

Allahabad

Bangalore

Barrackpore (W. B.)

· Central Inland Capture Fisheries Research Institute

Bhopal

Bhubaneswar

Calcutta

Chandigarh

Chennai (Madras)

Delhi

Dehradun

Dirang (Arunachal Pradesh)

Durgapur

Eluru (A. P.)

Gandhi Nagar

Goa

Hyderabad

Indore

Jammu

Jhansi (U. P)

Jodhpur (Rajasthan)

Kanpur

Kasaragod

Kharagpur

Kochi

Lucknow

Mathura

Mumbai (Bombay)

Palakkad

Palampur (H.P.)

Peechi

Pilani

Puttur (Karnataka)

Pune

Roorkie (U. P.)

Trivandrum (Thiruvananthapuram)

Varanasi (U. P.)

· Indian Institute of Vegetable Research

 

UNIVERSITIES/COLLEGES UNDER UGC

DST

•  Agharkar Research Institute, Pune

•  Birbal Sahni Institute of Palaeobotany, Lucknow

•  Bose Institute, Kolkata

•  Indian Association for the Cultivation of Science, Kolkata

•  International Advanced Research Centre for Powder Metallurgy and New Materials,
...esr ...Hyderabad

•  Indian Institute of Astrophysics, Bangalore

•  Indian Institute of Geomagnetism, Mumbai

•  Indian Institute of Tropical Meteorology, Pune

•  Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore

•  National Accreditation Board for Testing & Calibration Laboratories, New Delhi

•  Raman Research Institute, Bangalore

•  S.N. Bose National Centre for Basic Sciences, Kolkata

•  Sreechitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram

•  Technology Information, Forecasting & Assessment Council (TIFAC), New Delhi

•  Vigyan Prasar, New Delhi

 

Indian Council of Agricultural Research

  • National Bureaue of Soil Survey & Land Use Planning (NBSSLUP)
  • Central Research Institute for Jute & Allied Fibres (CRIJAF)
  • National Bureaue of Agriculturally Important Micro-Organisms (NBAIMO
  • Central Research Institute for Dryland Agriculture
]]> Jit https://bioinformaticsonline.com/videolist/watch/10659/gps-dna-tracking-university-of-sheffield Sat, 10 May 2014 04:33:28 -0500 https://bioinformaticsonline.com/videolist/watch/10659/gps-dna-tracking-university-of-sheffield <![CDATA[GPS DNA tracking - University of Sheffield]]> University of Sheffield geneticist and bioinformatics expert Dr Eran Elhaik demonstrates the power of his new DNA research, which allows people to discover their genetic homeland from 1000 years ago. Find out more about our biological research here http://www.sheffield.ac.uk/aps]]> https://bioinformaticsonline.com/view/119 Wed, 10 Jul 2013 14:35:34 -0500 https://bioinformaticsonline.com/view/119 <![CDATA[Which are the best statistical programming languages to study for a bioinformatician?]]> In Bio-informatics based genome sequencing and predicting metabolic pathways research jobs I used Matlab, SAS, SPSS, R and several Bioconductor packages. Matlab had a lot of powerful tools and was easy to use, whereas SPSS is for non-programmers and R need programming skills. I am wondering what other people think is best? or there might not be one specific language but a few that lend themselves best to Bio-informatics work that is math heavy and deals with a large amount of data.

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/10741/managing-and-analyzing-next-generation-sequence-data Sat, 10 May 2014 06:28:06 -0500 https://bioinformaticsonline.com/bookmarks/view/10741/managing-and-analyzing-next-generation-sequence-data <![CDATA[Managing and Analyzing Next-Generation Sequence Data]]> Centralized Bioinformatics Core Facilities provide shared resources for the computational and IT requirements of the investigators in their department or institution. As such, they must be able to effectively react to new types of experimental technology. Recently faced with an unprecedented flood of data generated by the next generation of DNA sequencers, these groups found it necessary to respond quickly and efficiently to the informatics and infrastructure demands. Centralized Facilities newly facing this challenge need to anticipate time and design considerations of necessary components, including infrastructure upgrades, staffing, and tools for data analyses and management ...

More at http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000369

Address of the bookmark: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000369

]]> Rahul Agarwal