<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/7568?offset=680 https://bioinformaticsonline.com/opportunity/view/35422/postdoc-at-jaypee-institute-of-information-technology-jiit-noida-department-of-biotechnology Fri, 02 Feb 2018 11:13:25 -0600 <![CDATA[PostDoc at Jaypee Institute of Information Technology (JIIT), Noida Department of Biotechnology]]> Lab of Dr. Rawal is supported by generous grants to build advanced applications in emerging areas of cancer genomics, network sciences, vaccine development and epidemiology. The lab has dedicated high end Xeon servers, desktops, & laptops for research purpose. Currently, there are several researchers (JRFs, B. Techs, M. Tech and PhDs) working on several challenging bioinformatics projects. In addition, Dr. Rawal has collaborations with reputed national and international research teams.

Dr. Rawal and his US based collaborators have recently secured grant for development of vaccine against an infectious disease agent. For this project, applications are invited for the posts of Post Doctoral Fellow/Research Scientist (One Position) for the following time-bound sponsored projects as per the details given below:

PI: Dr. Kamal Rawal, Biotechnology Department, JIIT, Noida.

Essential Qualification(s) for Post Doctoral Fellow/ Research Scientist:

We are seeking an individual with expertise in analyzing literature information, text mining, network biology, data integration, and modeling. Competitive candidates would also have programming experience in scripting languages with perl, C, C++, and R programming. This position requires a PhD in Computational Biology, Bioinformatics, Biostatistics, Physics or related fields, and evidence of scientific productivity through publications in international journals. Motivation to gain an in-depth understanding of biological phenomena is required. Applications should include a current CV and names of at least three references. Application packages and inquiries regarding this position can be sent to Dr. Kamal Rawal (bioinfocvatgmaildotcom and kamaldotrawalatgmaildotcom). Screening of applications will commence immediately and the position will remain open until filled. Candidates having master’s degree with extensive experience in IT industry or research can also be considered for this post.

Salary: Rs 50000 per month.

Duration: 2 years or upto the project duration.

Number of position: 1

Candidate may also fill the following form:

https://docs.google.com/…/1FAIpQLSdZoZ21ZoNRStEeL5…/viewform

http://tinyurl.com/bioinfocv2017

]]> https://bioinformaticsonline.com/pages/view/35805/python-learning-resources-for-bioinformatics-and-computational-biologist Fri, 02 Mar 2018 06:54:15 -0600 https://bioinformaticsonline.com/pages/view/35805/python-learning-resources-for-bioinformatics-and-computational-biologist <![CDATA[Python learning resources for bioinformatics and computational biologist !]]> Python is a general-purpose language, which means it can be used to build just about anything, which will be made easy with the right tools/libraries.

Professionally, Python is great for backend web development, data analysis, artificial intelligence, and scientific computing. Many developers have also used Python to build productivity tools, games, and desktop apps, so there are plenty of resources to help you learn how to do those as well.

For pros and cons visit http://www.bestprogramminglanguagefor.me/why-learn-python and http://bioinformaticsonline.com/discussion/view/459/python-vs-perl

More resources at https://github.com/CodementorIO/Python-Learning-Resources

Following are the list of useful python programming resources:

]]> Jit https://bioinformaticsonline.com/opportunity/view/8466/srf-position-in-computational-systems-biology-computational-biology-group-iiit-delhi Sun, 23 Feb 2014 20:56:08 -0600 <![CDATA[SRF position in Computational Systems Biology Computational biology Group, IIIT-Delhi]]> An opportunity to perform research in DST supported project that involves building of mathematical models to understand the functional relationship between circadian rhythms and memory formation under stressful condition. In this project, mathematical model of circadian rhythms based on gene regulatory mechanisms will be unified with the mathematical model of calcium signal transduction pathway to understand and predict the formation of fear memory under stressful conditions. The research scholar will spend full time on this project to build new models and expected to contribute significantly to prepare the results for publication and presentation, and to contribute to grant proposals.

Required Qualifications: Masters in physics/chemistry/mathematics (or) MTech in bioengineering, chemical (or) Masters in any traditional field of science with outstanding performance throughout the program. Candidate should have cleared GATE/UGC-CSIR examinations. Applicant should have done basic mathematics courses like calculus, differential equations, numerical analysis etc in their degree program and have obtained good grades in those courses. Knowledge of MATLAB and C or at least one traditional programming language is absolutely necessary. Strong inclination to understand biological concepts is a must for this research work as this project is about modeling biological systems.

Salary: A fixed salary of Rs 18000 PM including HRA will be paid.

Last date for application: This advertisement is open until suitable candidate is found for the project.

Preferred Qualifications: - Expertise in dynamical systems theory, bifurcation theory, numerical simulations, parameter estimation.

Independence and high motivation for carrying out interdisciplinary research. - Excellent communication skills and ability to work independently. - Good working habits.

Interested candidates should submit both curriculum vitae and statement of interest in PDF format to sriramk@iiitd.ac.in and should clearly mention in the subject "Application for SRF".

]]> https://bioinformaticsonline.com/pages/view/36603/learning-python-programming-a-bioinformatician-perspective Mon, 14 May 2018 16:33:03 -0500 https://bioinformaticsonline.com/pages/view/36603/learning-python-programming-a-bioinformatician-perspective <![CDATA[Learning Python Programming - a bioinformatician perspective !]]> Python Programming is a general purpose programming language that is open source, flexible, powerful and easy to use. One of the most important features of python is its rich set of utilities and libraries for data processing and analytics tasks. In the current era of big biological data, python and biopython is getting more popularity due to its easy-to-use features which supports big data processing.

In this tutorial series article, I will explore features and packages of python which are widely used in the big data, NGS, and bioinformatics. I will also walk through a real biological example which shows NGS data processing with the help of python packages and programming.

Python has a couple of points to recommend it to biologists and scientists specifically:

  • It's widely used in the scientific community
  • It has a couple of very well designed libraries for doing complex scientific computing (although we won't encounter them in this book)
  • It lend itself well to being integrated with other, existing tools
  • It has features which make it easy to manipulate strings of characters (for example, strings of DNA bases and protein amino acid residues, which we as biologists are particularly fond of)

In general, following are some of the important features of python which makes it a perfect fit for rapid application development.

  • Python is interpreted language so the program does not need to be compiled. Interpreter parses the program code and generates the output.
  • Python is dynamically typed, so the variables types are defined automatically.
  • Python is strongly typed. So the developers need to cast the type manually.
  • Less code and more use makes it more acceptable.
  • Python is portable, extendable and scalable.

There are two major Python versions, Python 2 and Python 3. Python 2 and 3 are quite different. This tutorial uses Python 3, because it more semantically correct and supports newer features.

I will post tutorial on daily basis on this page. Check the sub-pages on right side.

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/39370/multiphate-bioinformatics-pipeline-for-functional-annotation-of-phage-isolates Thu, 16 May 2019 00:17:39 -0500 https://bioinformaticsonline.com/bookmarks/view/39370/multiphate-bioinformatics-pipeline-for-functional-annotation-of-phage-isolates <![CDATA[multiPhATE: bioinformatics pipeline for functional annotation of phage isolates]]> multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene-calling algorithm and assigns putative functions to gene calls using protein-, virus-, and phage-centric databases. 

 

Address of the bookmark: https://github.com/carolzhou/multiPhATE

]]> Abhimanyu Singh https://bioinformaticsonline.com/pages/view/9030/linux-ssh-client-commands-for-bioinformatics Thu, 13 Mar 2014 17:16:32 -0500 https://bioinformaticsonline.com/pages/view/9030/linux-ssh-client-commands-for-bioinformatics <![CDATA[Linux SSH Client Commands for Bioinformatics]]> Here come on let play with the following basic command line usage of the ssh client.

1. Check your SSH Client Version:

Checking for your SSH client is very sare, but sometimes it may be necessary to identify the SSH client that you are currently running and it’s corresponding version number. The SSh client can be identified as follows

$ ssh -V
OpenSSH_3.9p1, OpenSSL 0.9.7a Feb 19 2013

$ ssh -V
ssh: SSH Secure Shell 3.2.9.1 (non-commercial version) on i686-pc-linux-gnu

2. Connect and login to remote host:

The First time when you login to the remotehost from a localhost, it will display the host key not found message and you can give “yes” to continue. The host key of the remote host will be added under .ssh2/hostkeys directory of your home directory, as shown below.

localhost$ ssh -l jit remotehost.example.com

jit@remotehost.example.com password:

remotehost.example.com$

The Second time when you login to the remote host from the localhost, it will prompt only for the password as the remote host key is already added to the known hosts list of the ssh client.

localhost$ ssh -l jit remotehost.example.com
jit@remotehost.example.com password:
remotehost.example.com$

For some reason, if the host key of the remote host is changed after you logged in for the first time, you may get a warning message as shown below. This could be because of various reasons such as 1) Sysadmin upgraded/reinstalled the SSH server on the remote host 2) someone is doing malicious activity etc., The best possible action to take before saying “yes” to the message below, is to call your sysadmin and identify why you got the host key changed message and verify whether it is the correct host key or not.

localhost$ ssh -l jit remotehost.example.com

jit @remotehost.example.com's password:
remotehost$

4. Debug SSH Client:

Sometimes it is necessary to view debug messages to troubleshoot any SSH connection issues. For this purpose, pass -v (lowercase v) option to the ssh as shown below.

Example without debug message:

        localhost$ ssh -l jit remotehost.example.com
        warning: Connecting to remotehost.example.com failed: No address associated to the name
        localhost$

Example with debug message:

        locaclhost$ ssh -v -l jit remotehost.example.com
        debug: SshConfig/sshconfig.c:2838/ssh2_parse_config_ext: Metaconfig parsing stopped at line 3.
        debug: SshConfig/sshconfig.c:637/ssh_config_set_param_verbose: Setting variable 'VerboseMode' to 'FALSE'.
        debug: SshConfig/sshconfig.c:3130/ssh_config_read_file_ext: Read 17 params from config file.
        debug: Ssh2/ssh2.c:1707/main: User config file not found, using defaults. (Looked for '/home/jit/.ssh2/ssh2_config')
        debug: Connecting to remotehost.example.com, port 22... (SOCKS not used)
        warning: Connecting to remotehost.example.com failed: No address associated to

5. Escape Character: (Toggle SSH session, SSH session statistics etc.)

Escape character ~ get’s SSH clients attention and the character following the ~ determines the escape command.
Toggle SSH Session: When you’ve logged on to the remotehost using ssh from the localhost, you may want to come back to the localhost to perform some activity and go back to remote host again. In this case, you don’t need to disconnect the ssh session to the remote host. Instead follow the steps below.

i. Login to remotehost from localhost: localhost$ssh -l jit remotehost
ii. Now you are connected to the remotehost: remotehost$
iii. To come back to the localhost temporarily, type the escape character ~ and Control-Z. When you type ~ you will not see that immediately on the screen until you press and press enter. So, on the remotehost in a new line enter the following key strokes for the below to work: ~

    remotehost$ ~^Z
    [1]+  Stopped                 ssh -l jit remotehost
    localhost$

iv. Now you are back to the localhost and the ssh remotehost client session runs as a typical unix background job, which you can check as shown below:

    localhost$ jobs
    [1]+  Stopped                 ssh -l jit remotehost

v. You can go back to the remote host ssh without entering the password again by bringing the background ssh remotehost session job to foreground on the localhost

    localhost$ fg %1
    ssh -l jit remotehost
    remotehost$

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/40272/seq-a-high-performance-pythonic-language-for-bioinformatics Sat, 23 Nov 2019 08:58:12 -0600 https://bioinformaticsonline.com/bookmarks/view/40272/seq-a-high-performance-pythonic-language-for-bioinformatics <![CDATA[Seq: A high-performance, Pythonic language for bioinformatics]]>  

Seq is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host of domain-specific features and optimizations, Seq makes writing high-performance genomics software as easy as writing Python code, and achieves performance comparable to (and in many cases better than) C/C++.

Learn more by following the tutorial or from the cookbook.

Address of the bookmark: https://seq-lang.org

]]> Rahul Nayak https://bioinformaticsonline.com/file/view/9213/basic-notions-in-molecular-biology-and-genetics Sun, 16 Mar 2014 18:15:29 -0500 https://bioinformaticsonline.com/file/view/9213/basic-notions-in-molecular-biology-and-genetics <![CDATA[Basic Notions in Molecular Biology and Genetics]]> This is a presentation about some fundamental concepts applied in molecular biology and genetics, also it contains a little bit of the experience that one of our members has gained in his years of undergraduate state related to molecular cloning. Our research group, called "BIOPHARM" (Acronymus of Laboratory of Bioinformatics and Pharmacogenetics), was stablished on 2007, took it a bit of years to make it real this initative, although, nowadays, we're working on some projects involved in those fields. This research group belongs to the Department of Biochemistry, Faculty of Pharmacy and Biochemistry, Universidad Nacional Mayor de San Marcos, Lima, Perú. We try to encourage research initiatives, helping them and also we use to participate in differents courses, congress and symposiums.

]]> Antony Campos https://bioinformaticsonline.com/bookmarks/view/40959/bioinformatics-related-group Sun, 09 Feb 2020 03:17:16 -0600 https://bioinformaticsonline.com/bookmarks/view/40959/bioinformatics-related-group <![CDATA[Bioinformatics related group]]> FaBI emerged from the respective groups of the four founding societies GI (German Informatics Society), DECHEMA (Society for Chemical Engineering and Biotechnology), GBM (Society for Biochemistry and Molecular Biology) and GDCh (German Chemical Society). In fall 2015, the GMDS (German Society for Medical Informatics, Biometry, and Epidemiology) joined FaBI. FaBI represents more than 750 members today and considers itself as a joint representation of interests of bioinformatics research in Germany and as an interlocutor for politics, economy, and society aiming at a strong informatics-based life science research.

Address of the bookmark: https://bioinformatik.de/en/bioinformatics-in-germany/research/research-groups.html

]]> Rahul Agarwal https://bioinformaticsonline.com/opportunity/view/42158/rgcb-recruitment-notification-for-bioinformatician Tue, 25 Aug 2020 00:25:13 -0500 <![CDATA[RGCB recruitment notification for bioinformatician !]]> RGCB Jobs 2020: RGCB released the recruitment notification to hire the candidates who completed B.Tech, M.Sc for 01 Bioinformatician Posts. The eligible candidates can apply for the post through online from 22-08-2020 to 08-09-2020. These selected candidates will be placed as Bioinformatician in Kerala. To know more details such as salary (pay scale), age limit, application fee, application process and more for RGCB recruitment 2020 by clicking apply button.
Organization Name : Rajiv Gandhi Centre for Biotechnology
Post Name : Bioinformatician
No of Vacancy : 01 Posts
Salary : Rs.22,000 (Per Month)
Last Date to Apply : 08-09-2020

More at https://rgcb.res.in/jobs.php

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