BOL: Related items

Senior Scientist Computational Biology at NIPGR

Sun, 19 Jul 2020 23:30:04 -0500

Senior Scientist Computational Biology
Level 13

₹ 1,66,378 (Consolidated)

(UR)

Ph.D. in the area of Computational Biology/Bioinformatics/Biotechnology/Life Sciences with at least 6 years of relevant experience.
OR
M. Tech with 8 years of relevant experience.

The relevant experience shall be in the area of sequencing/genome assembly and annotation and high throughput genotyping for facilitating Genomic assisted Breeding
Age: Not exceeding 50 years

• The incumbent will assist the Programme Director of the Facility to discharge various activities of the NGGF

• Co-ordination with the service provider, DBT/academic institutions/anchoring institute (NIPGR) for execution of activities of the Facility.

• The incumbent will be expected to identify the requirements of Private Sector and Government laboratories in the area of Marker assisted selection and develop linkages to facilitate the same.

• Interact with multiple stake holders including Government and Private Sector in the area of agriculture Biotechnology.

• Oversee the establishment of relevant Standard Operational Procedures (SOP), Quality Accreditation of Genomics and Genotyping facility.

More at http://www.nipgr.ac.in/careers/vacancies_latest.php#vacancy2

3 PhD positions available in the area of Bioinformatics/Computational Biology at ulster.ac.uk

Thu, 02 Jan 2020 12:41:10 -0600

3 PhD positions available in the area of Bioinformatics/Computational Biology, Machine Learning (ML)/Artificial Intelligence (AI), Biomarker Discovery, Stratified/Personalized Medicine in Mental Health, Diabetes and Multimorbidity. Please see details (weblinks) below:

1. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/510894
2. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/511458
3. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/512618

Looking for students with good computational/programming skills (preferable in Linux/Shell, Python and/or R) and knowledge in computational biology and statistics. However, students from more biology oriented background but strong interest to learn bioinformatics and programming are also encouraged to apply.

Informal inquiries are welcomed at: p.shukla@ulster.ac.uk

Dr Priyank Shukla PhD FHEA FCHERP
Lecturer (Asst Prof) in Stratified Medicine (Bioinformatics)

Northern Ireland Centre for Stratified Medicine
Biomedical Sciences Research Institute
University of Ulster (Magee Campus)
C-TRIC Building, Altnagelvin Area Hospital
Glenshane Road, Derry/Londonderry
BT47 6SB, Northern Ireland, United Kingdom

T: +44 28 7167 5690
E: p.shukla@ulster.ac.uk
W: https://www.ulster.ac.uk/staff/p-shukla

A computational postdoc position and a bioinformatician position

Thu, 18 Jan 2018 16:29:42 -0600

A computational postdoc position and a bioinformatician position are available in Alessandro Romanel's Lab recently established at the Centre for Integrative Biology (CIBIO) in Trento, Italy. The positions are in the context of an AIRC grant and are immediately available.

Successful candidates will be involved in the design and implementation of strategies to study the role of inherited polymorphisms in combination with timedependent variables and somatic events on cancer genesis, progression and resistance.
The ideal postdoc candidate will have a PhD in Computer Science, Bioinformatics, Computational Biology or equivalent, experience in the analysis of next generation sequencing and high-density array data from human cells, strong analytical and quantitative background and programming skills. Background in cancer genomics is recommended.
The ideal bioinformatician candidate will have a four or five years degree in Computer Science, Bioinformatics or equivalent, experience in the management of large datasets, implementation of processing pipelines and strong programming skills. Background in biology/genomics is a plus.
Highly motivated individuals are invited to send a detailed CV, a cover letter describing research interests and experience, and contact information for two references to Alessandro Romanel (alessandro.romanel@unitn.it).

iRNAD: a computational tool for identifying D modification sites in RNA sequence

Abhimanyu Singh — Thu, 16 May 2019 00:20:07 -0500

iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the classification.

http://lin-group.cn/server/iRNAD/

Address of the bookmark: http://lin-group.cn/server/iRNAD/

SCFBio have developed Sanjeevini

Jit — Fri, 17 Nov 2017 07:55:49 -0600

SCFBio have developed a new android based application for drug design called Sanjeevini (https://play.google.com/store/apps/details?id=com.sanjeevini&hl=en). It is available free of charge. You can download it using Google play store. Just search for "Sanjeevini-SCFBIO-CADD" in Google play store. It contains all modules used by current Sanjeevini users. We have worked towards making a unified and easy to use interface. The app now supports all major small molecule file formats (pdb, mol, sdf, mol2 and xyz). The application contains inbuilt visualizer JSmol for easy analysis of results. Users can now directly download the protein files from PDB ("Get protein PDB file" in `FILE` Menu) and prepare it using the easy to use in-built module "Prepare protein/DNA".

SCFBio have worked towards making the process of Job retrieval more streamlined and user friendly. All jobs are now recorded in the "Job results". It can be accessed using the main page of the application. Job status can now be retrieved by clicking on the refresh button against the job ID.

SCFBio have also added a new feature of accessing Jobs run on different android application. Users can retrieve jobs run by other users by sharing the job ID and module name. This feature can be accessed using the Import Jobs option in File menu. We hope this feature will help collaborating groups stay in touch with each other.

The module contains all modules of Sanjeevini suite of software for structure based Drug design.

Sl No.	Module name	Activity
1	Prepare Protein/DNA	Prepares protein/DNA for other modules of Sanjeevini
2	Prepare ligand	Prepares ligands for other modules of Sanjeevini
3	Active site Prediction	Predicts biologically relevant sites in a protein
4	ParDOCK	Rigid Docking of Protein-Ligand complex
5	BAPPL	Binding affinity prediction of Protein-Ligand complex
6	BAPPL Z	Binding affinity prediction of Protein-Zinc-Ligand complex
7	DNA ligand Docking	Rigid Docking of DNA-Ligand complex
8	PreDDICTA	Binding affinity prediction of DNA-Ligand complex
9	SOM Prediction	Rigid Docking of Ligand and CYP proteins
10	Lipinski filters	Checks Lipinski's rule of five for ligand molecule
11	Molecular volume	Calculates volume of a ligand
12	RASPD	Virtual screening of protein molecule to yield hit molecules
13	AADS	Prediction and docking of top 10 biologically relevant sites on protein
14	Intercalate	Rigid Docking of DNA-Ligand complex in intercalation sites
15	DNA sequence to str.	Converts DNA sequence to DNA structure (A-DNA or B-DNA)
16	NRDBSM	Non-redundant database of small molecules
17	TPACM4	Partial charge calculator for small molecules
18	Wiener index	Wiener index calculator for small molecules

The results can be downloaded to the PC desktop for further analysis. For this you can use this accompanying website for this purpose:
http://www.scfbio-iitd.res.in/sanjapp/webSearch/Sanjeevini_webpage.html

On more information on how to use the application please visit: http://scfbio-iitd.res.in/sanjapp/webSearch/doc.html
or
http://scfbio-iitd.res.in/sanjeeviniapp/tut.html

Please email us your valuable comments and suggestions at iitd.scfbio@gmail.com

Mobyle: a new full web bioinformatics framework

Jit — Sun, 07 Jan 2018 19:33:45 -0600

Mobyle, to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software.

Address of the bookmark: https://academic.oup.com/bioinformatics/article/25/22/3005/179064

nQuire: a statistical framework for ploidy estimation using next generation sequencing

Jit — Thu, 04 Oct 2018 05:23:59 -0500

nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuireunder the MIT license.

Address of the bookmark: https://github.com/clwgg/nQuireunder

ALF--a simulation framework for genome evolution.

Jit — Tue, 22 Oct 2019 22:05:58 -0500

Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A description of ALF can be found in the following article:

Daniel A Dalquen, Maria Anisimova, Gaston H Gonnet, Christophe Dessimoz: ALF - A Simulation Framework for Genome Evolution. Mol Biol Evol, 29(4):1115-1123, April 2012.
http://mbe.oxfordjournals.org/content/29/4/1115

Address of the bookmark: http://alfsim.org/#index

Visiting Scientist - Computational Genomics

Mon, 17 Jul 2017 07:20:18 -0500

ICRISAT is a non-profit, non-political organization that conducts agricultural research for development in Asia and sub-Saharan Africa with a wide array of partners throughout the world. ICRISAT and its partners help empower those living in the semi-arid tropics, especially smallholder farmers, to overcome poverty, hunger, malnutrition and a degraded environment through more efficient and profitable agriculture.

ICRISAT is headquartered in Patancheru near Hyderabad, India, with two regional hubs and five country offices in sub-Saharan Africa. ICRISAT, established in 1972, is a member of the CGIAR Consortium. For more details, see www.icrisat.org.

Job Responsibilities:
Planning and execution of different NGS/genomics data analysis
Apply, maintain, and support cutting-edge pipelines for the analysis and interpretation of NGS data
Analyze large-scale genomic datasets generated internally and through collaboration with others
Genome wide analysis- LD analysis, hapmap, genetic map construction and qtl mapping
Expression analysis based on RNA-seq, gene ontology and metabolic pathway data
Sequence level analysis like gene family analysis, orthology/paralogy etc.
Familiarity with genomic and biological information databases
Compilation and interpretation of results and writing reports
Experience working independently and in a team environment
Requirements:

PhD or M.Sc with 2-3 years experience from reputed institute in the area of life science or similar Knowledge in Next Generation Sequencing (NGS) data analysis. Should be familiar with various sequencing platforms. Sound knowledge of genomics and molecular biology is must. Proficient in any one of the programming/scripting in languages: Python, Perl, PHP, R, Shell Scripting. Must be experienced in working on Linux and CLI environment. Ability to work as team as well as independently with minimal support. Fluency in spoken and written English is essential.

NGS techniques like sequence alignment, variant calling based on whole genome re-sequencing and genotyping-by-sequencing (GBS), RNA-Seq/transcriptome analysis
Knowledge of various standard NGS related tool
Ability to solve complex problems in advanced genomics research areas
Ease and interest in working with people from diverse backgrounds
Excellent oral/written communication and interpersonal/networking skills
General:
This position is contract for a period of two years.

How to apply:
Applicants should apply on or before 27-July-2017, with latest Curriculum Vitae, and the names and contact information of three references that are knowledgeable about your professional qualifications and work experience. All applications will be acknowledged, however only short listed candidates will be contacted
Please CLICK HERE to submit your application.
ICRISAT is an equal opportunity employer

http://icrisat.careersitemanager.com/job-listings-Visiting-Scientist-Computational-Genomics-ICRISAT-Hyderabad-Secunderabad-2-to-4-years-060717000278

Linux Commands Cheat Sheet for Bioinformatics and Computational Biology Professionals

Rahul Nayak — Mon, 05 Feb 2018 18:50:41 -0600

The purpose of this cheat sheet is to introduce biologist and bioinformatician to the frequently used tools for NGS analysis as well as giving experience in writing one-liners.

File System
ls — list items in current directory
ls -l — list items in current directory and show in long format to see perimissions, size, and modification date
ls -a — list all items in current directory, including hidden files
ls -F — list all items in current directory and show directories with a slash and executables with a star
ls dir — list all items in directory dir
cd dir — change directory to dir
cd .. — go up one directory
cd / — go to the root directory
cd ~ — go to to your home directory
cd - — go to the last directory you were just in
pwd — show present working directory
mkdir dir — make directory dir
rm file — remove file
rm -r dir — remove directory dir recursively
cp file1 file2 — copy file1 to file2
cp -r dir1 dir2 — copy directory dir1 to dir2 recursively
mv file1 file2 — move (rename) file1 to file2
ln -s file link — create symbolic link to file
touch file — create or update file
cat file — output the contents of file
less file — view file with page navigation
head file — output the first 10 lines of file
tail file — output the last 10 lines of file
tail -f file — output the contents of file as it grows, starting with the last 10 lines
vim file — edit file
alias name 'command' — create an alias for a command
System
shutdown — shut down machine
reboot — restart machine
date — show the current date and time
whoami — who you are logged in as
finger user — display information about user
man command — show the manual for command
df — show disk usage
du — show directory space usage
free — show memory and swap usage
whereis app — show possible locations of app
which app — show which app will be run by default
Process Management
ps — display your currently active processes
top — display all running processes
kill pid — kill process id pid
kill -9 pid — force kill process id pid
Permissions
ls -l — list items in current directory and show permissions
chmod ugo file — change permissions of file to ugo - u is the user's permissions, g is the group's permissions, and o is everyone else's permissions. The values of u, g, and o can be any number between 0 and 7.
7 — full permissions
6 — read and write only
5 — read and execute only
4 — read only
3 — write and execute only
2 — write only
1 — execute only
0 — no permissions
chmod 600 file — you can read and write - good for files
chmod 700 file — you can read, write, and execute - good for scripts
chmod 644 file — you can read and write, and everyone else can only read - good for web pages
chmod 755 file — you can read, write, and execute, and everyone else can read and execute - good for programs that you want to share
Networking
wget file — download a file
curl file — download a file
scp user@host:file dir — secure copy a file from remote server to the dir directory on your machine
scp file user@host:dir — secure copy a file from your machine to the dir directory on a remote server
scp -r user@host:dir dir — secure copy the directory dir from remote server to the directory dir on your machine
ssh user@host — connect to host as user
ssh -p port user@host — connect to host on port as user
ssh-copy-id user@host — add your key to host for user to enable a keyed or passwordless login
ping host — ping host and output results
whois domain — get information for domain
dig domain — get DNS information for domain
dig -x host — reverse lookup host
lsof -i tcp:1337 — list all processes running on port 1337
Searching
grep pattern files — search for pattern in files
grep -r pattern dir — search recursively for pattern in dir
grep -rn pattern dir — search recursively for pattern in dir and show the line number found
grep -r pattern dir --include='*.ext — search recursively for pattern in dir and only search in files with .ext extension
command | grep pattern — search for pattern in the output of command
find file — find all instances of file in real system
locate file — find all instances of file using indexed database built from the updatedb command. Much faster than find
sed -i 's/day/night/g' file — find all occurrences of day in a file and replace them with night - s means substitude and g means global - sed also supports regular expressions
Compression
tar cf file.tar files — create a tar named file.tar containing files
tar xf file.tar — extract the files from file.tar
tar czf file.tar.gz files — create a tar with Gzip compression
tar xzf file.tar.gz — extract a tar using Gzip
gzip file — compresses file and renames it to file.gz
gzip -d file.gz — decompresses file.gz back to file
Shortcuts
ctrl+a — move cursor to beginning of line
ctrl+f — move cursor to end of line
alt+f — move cursor forward 1 word
alt+b — move cursor backward 1 word