<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/27461?offset=160 https://bioinformaticsonline.com/researchlabs/view/22761/pit-bioinformatics-group Tue, 16 Jun 2015 14:34:26 -0500 <![CDATA[PIT Bioinformatics Group]]> PIT Bioinformatics Group solves problems in bioinformatics and computational biology. Recent developed online tools:

- Budapest Reference Connectome: View a parametrizable connectome (brain graph).
- AmphoraNet: The webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data.
- AmphoraVizu: Chart visualization for metagenomics analysis tools AMPHORA2 and AmphoraNet.
- SCARF: Free online association rule mining tool.

More at: http://pitgroup.org

]]> https://bioinformaticsonline.com/researchlabs/view/7212/bioinformatics-group-at-boku-university Thu, 12 Dec 2013 17:53:10 -0600 <![CDATA[Bioinformatics group at Boku University]]> The Bioinformatics group at Boku University has two main areas of interest, underpinning a common goal, the study of complex systems in living organisms. To overcome the engineered redundancies and combinatorial effects prevalent in higher eukaryotes, novel views augmenting the classical gene by gene approaches are required. We combine

1. Work to establish improved quantitative experimental assays (such as microarrays or differential in-gel electrophoresis) and
2. Development of modern computational methods (such as hierarchical probabilistic models or integration of heterogeneous data sources)

Lab page @ http://bioinf.boku.ac.at/

]]> https://bioinformaticsonline.com/bookmarks/view/23498/algorithms-for-dna-sequencing-course-offered-each-month Sun, 26 Jul 2015 01:57:02 -0500 https://bioinformaticsonline.com/bookmarks/view/23498/algorithms-for-dna-sequencing-course-offered-each-month <![CDATA[Algorithms for DNA Sequencing (course offered each month)]]> "We will learn computational methods -- algorithms and data structures -- for analyzing DNA sequencing data. We will learn a little about DNA, genomics, and how DNA sequencing is used. We will use Python to implement key algorithms and data structures and to analyze real genomes and DNA sequencing datasets."

Source : https://www.coursera.org/course/ads1

 

Address of the bookmark: https://www.coursera.org/course/ads1

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/7216/free-math-books Thu, 12 Dec 2013 19:38:34 -0600 https://bioinformaticsonline.com/bookmarks/view/7216/free-math-books <![CDATA[Free math books]]> Bioinformatics require some match skills, therefore I decided to provide this wonderful math eBooks links to the BOL community.

Please add ur links/bookmarks in comment section.

Address of the bookmark: http://physicsdatabase.com/free-math-books/

]]> Manisha Mishra 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/bookmarks/view/7387/bioinformatics-software-for-biologists-in-the-genomics-era Sun, 22 Dec 2013 17:31:05 -0600 https://bioinformaticsonline.com/bookmarks/view/7387/bioinformatics-software-for-biologists-in-the-genomics-era <![CDATA[Bioinformatics software for biologists in the genomics era]]> The genome sequencing revolution is approaching a landmark figure of 1000 completely sequenced genomes. Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data has encouraged laboratory scientists to engage large datasets in comparative sequence analyses for making evolutionary, functional and translational inferences. However, the majority of the scientists at the forefront of experimental research are not bioinformaticians, so a gap exists between the user-friendly software needed and the scripting/programming infrastructure often employed for the analysis of large numbers of genes, long genomic segments and groups of sequences. We see an urgent need for the expansion of the fundamental paradigms under which biologist-friendly software tools are designed and developed to fulfill the needs of biologists to analyze large datasets by using sophisticated computational methods. We argue that the design principles need to be sensitive to the reality that comparatively small teams of biologists have historically developed some of the most popular biological software packages in molecular evolutionary analysis. Furthermore, biological intuitiveness and investigator empowerment need to take precedence over the current supposition that biologists should re-tool and become programmers when analyzing genome scale datasets.

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/23/14/1713.full

]]> Poonam Mahapatra 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/7753/jrf-pondicherry-university Fri, 03 Jan 2014 16:48:56 -0600 <![CDATA[JRF @ PONDICHERRY UNIVERSITY]]> PONDICHERRY UNIVERSITY

CENTRE FOR BIOINFORMATICS

PUDUCHERRY

Applications are invited for one Project Assistant to work in the UGC sponsored Research Award "Molecular Docking and Dynamics studies to understand the interacting mechanism of oncogenic 101 protein with its cellular proteins".

The duration for the fellowship is 12months only with consolidated pay ofRs. 5,000 per month.

Application on plain paper with following details: Name, Address, Data of Birth, Father's Name, Nationality, Educational Qualification (SSLC onwards-enclose attested copies of certificate) and Researcb Experience may be addressed to Dr. R. Krishna, Principle Investigator (PI), UGC Research Award, Centre for Bioinformatics, Pondicherry University, Pondicherry - 605 014.

Application should reach in January 261h , 2013.

Essential Qualification: M.Sc. in Bioinformatics/Biophysics with good academic record.

Qualification for Project Fellow:

M.Sc in Bioinformatics/Biophysics.

The person to be considered for appointment as Project Fellow must have second class master degree with a minimum of 55% marks in the subject concerned or a related subject.

The candidate to be appointed as Project Fellows should be below thc age of40 years at the time of appointment.

Desirable Qualification for this Project: Research Experience in Small/Macromolecule Crystallography and Structural Bioinformatics.

For more details, refer the web site: www.pondiuni.edu.in/sites/default/files/BIC-311213.pdf

]]> 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/opportunity/view/7998/faculty-positions-at-iiit-allahabad Thu, 23 Jan 2014 06:19:34 -0600 <![CDATA[FACULTY POSITIONS AT IIIT-ALLAHABAD]]> OPENINGS OF FACULTY POSITIONS AT IIIT-ALLAHABAD

(Under Tenure-Track Model)

Open Advt. No IIITA/DIC/16012014

IIIT-Allahabad has several Openings for the Faculty positions at the Assistant Professor level.

It is a regular tenure-track faculty positions for 3-5 years in teaching and research. A regular faculty is expected to engage heavily in research and teaching. The eligibility criteria for regular faculty positions are similar as in IITs. For an Assistant Professor position, a candidate must have a PhD (in IT/Computer Science &/or Engineering/Electrical, Electronics &/or Communication Engineering/etc; for interdisciplinary areas the PhD may be in an appropriate field), plus three years experience. However, for PhDs from a well known University/Institute (e.g. IITs/IISc/TIFR/ISI in India or well known research universities across the world), and a good research/academic record, the 3 years experience requirement may be waived.

The pay scale for faculty is same as in IITs. Other benefits include initiation research grant, travel support, book grant, professional society membership, etc., and personal benefits such as medical/LTC, on campus subsidized family housing with excellent modern infrastructural facilities.

Areas of Interest

IIIT-Allahabad aims to build strong research groups in important and emerging areas in CS/IT/ECE as well as in emerging interdisciplinary areas, and applications are invited in all these areas. Some of the areas of special interest, besides strengthening the existing research areas, are : Software Engineering, Theoretical Computer Science, Cyber Physical Systems, Robotics, Network science, Digital Media, Computational neuroscience, Machine learning, Healthcare informatics, Computational Biology, Communications networks (both at hardware and protocol levels), Circuits (including VLSI, analog, low power, etc), Energy systems and technologies, Biomedical electronics and systems, Computer Architecture, signal/image processing, Embedded and control systems.

Application Process

Interested candidates can apply by sending their detailed CV with list of publications clearly mentioning Journal names and citation index with three references through email entitled “Faculty positions at IIIT Allahabad” to faculty.applications@iiita.ac.in. Do not send your applications in any other email addresses. Applications will be considered regularly, hence there is no deadline for applying.

Important Clarifications on Eligibility

A PhD in CS/IT (or other disciplines, as announced) is the minimum expected requirement for an Assistant Professor.

Advertisement: http://iiita.ac.in/pub/Faculty-Position-IIITA1.pdf

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