<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/42813?offset=20 https://bioinformaticsonline.com/bookmarks/view/26332/pilon Mon, 08 Feb 2016 15:56:18 -0600 https://bioinformaticsonline.com/bookmarks/view/26332/pilon <![CDATA[Pilon]]> Pilon is a software tool which can be used to:

  • Automatically improve draft assemblies
  • Find variation among strains, including large event detection

Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:

  • Single base differences
  • Small indels
  • Larger indel or block substitution events
  • Gap filling
  • Identification of local misassemblies, including optional opening of new gaps

More at https://github.com/broadinstitute/pilon/wiki

Address of the bookmark: https://github.com/broadinstitute/pilon/wiki

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/28200/machine-learning Fri, 01 Jul 2016 12:57:12 -0500 https://bioinformaticsonline.com/bookmarks/view/28200/machine-learning <![CDATA[Machine Learning !!!]]> In machine learning, computers apply statistical learning techniques to automatically identify patterns in data. These techniques can be used to make highly accurate predictions.

Keep scrolling. Using a data set about homes, we will create a machine learning model to distinguish homes in New York from homes in San Francisco.

Address of the bookmark: http://www.r2d3.us/visual-intro-to-machine-learning-part-1/

]]> Gudiya Pal https://bioinformaticsonline.com/bookmarks/view/35798/an-introduction-to-applied-bioinformatics Fri, 02 Mar 2018 04:26:38 -0600 https://bioinformaticsonline.com/bookmarks/view/35798/an-introduction-to-applied-bioinformatics <![CDATA[An Introduction to Applied Bioinformatics]]> IAB is primarily being developed by Greg Caporaso(GitHub/Twitter: @gregcaporaso) in the Caporaso Lab at Northern Arizona University. You can find information on the courses I teach on my teaching website and information on my research and lab on my lab website.

 

Address of the bookmark: http://readiab.org/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37636/department-of-genetics-genomics-and-bioinformatics-national-biotechnology-development-agency-nigeria Wed, 05 Sep 2018 10:48:25 -0500 https://bioinformaticsonline.com/bookmarks/view/37636/department-of-genetics-genomics-and-bioinformatics-national-biotechnology-development-agency-nigeria <![CDATA[DEPARTMENT OF GENETICS, GENOMICS AND BIOINFORMATICS, National Biotechnology Development Agency, Nigeria]]> The Genetics, Genomics & Bioinformatics Department (GBBD) at NABDA is unique, encompassing all facets of modern genetics and bioinformatics research. Trans-disciplinary research being conducted in our laboratories would lead to cures for human diseases; improvements to crop and livestock quality and yield; creation of new technologies with applications to medicine; agriculture; environment; and industry.

Our capacity building activities covers both general and specialized topics in translational genetics, and is designed to better acquaint scientists and clinicians with the tools and technologies of genetics and genomics.

OUR RESEARCH ACTIVITIES INCLUDE:

  • Biomedical Genetics: investigating genetic and environmental factors contributing to phenotypes with relevance to human health and disease.
  • Computation and Bioinformatics: develop new approaches for the management, analysis, and modelling of large, complex data sets.
  • Population and Quantitative Genetics: study of how genetic processes evolve to generate genetic variation in populations of organisms, and the effects on the patterning of variation within and between populations and specie, and
  • Genetic Engineering and Biotechnology: focuses on the research and innovation for industrial enzymes, biologics and biosimilars production.

https://www.h3abionet.org/nabda

Address of the bookmark: http://www.nabda.gov.ng/departments/genetics-genomics-and-bioinformatics

]]> BioStar https://bioinformaticsonline.com/pages/view/42810/bioinformatics-in-africa-part3-mali Sat, 06 Feb 2021 13:28:44 -0600 https://bioinformaticsonline.com/pages/view/42810/bioinformatics-in-africa-part3-mali <![CDATA[Bioinformatics in Africa: Part3 - Mali]]> International Center for Excellence in Research (ICER):

The ICER is a research center composed of the following three programs: 1. The Malaria Research and Training Center ­ Parasitology Group,  2. The Malaria Research and Training Center ­ Entomology Group  3. The SEREFO Group.

The first two programs develop biomedical researches in malaria, Filariasis and Leishmaniasis. The  third program develops biomedical researches in tuberculosis and HIV.

Bioinformatics was introduced recently to the ICER and is constantly growing. The ICER has one  team, headed by Sidy SOUMARE, which supports the three programmes in all their needs in  informatics and bioinformatics. This team can beneficiate from some computational facilities (4  blast servers, 15 other servers and around 200 terminals), but the ICER staff needs some training in  order to be able to administrate these facilities.

Research Interest and Activities: The following are the present areas of research interest: 1. Functional genomics 2. Analysis of microarray data 3. Interaction between the vector and the parasite.

]]> BioStar 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/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/43243/interactive-bioinformatics-resources Thu, 12 Aug 2021 00:09:00 -0500 https://bioinformaticsonline.com/bookmarks/view/43243/interactive-bioinformatics-resources <![CDATA[Interactive Bioinformatics Resources !]]> Learn how to use bioinformatics tools right from your browser.
Everything runs in a sandbox, so you can experiment all you want.

More at sandbox.bio

Address of the bookmark: http://sandbox.bio

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44403/programming-for-lovers Tue, 07 Nov 2023 23:56:30 -0600 https://bioinformaticsonline.com/bookmarks/view/44403/programming-for-lovers <![CDATA[Programming for Lovers !]]> Programming for Lovers (P4❤️) is a free online course that teaches programming using the Go programming language by immersing learners in fun scientific applications.

Each chapter focuses on a single scientific problem and contains a core text accompanied by code alongs and autograded exercises.

You can meet Phillip Compeau in our intro video. Phillip has taught programming at Carnegie Mellon University for years and is a serial online education founder. He is thrilled to bring you this course.

Address of the bookmark: https://programmingforlovers.com/

]]> BioStar https://bioinformaticsonline.com/news/view/20440/linux-operating-system-aimed-at-scientists Mon, 19 Jan 2015 08:30:49 -0600 https://bioinformaticsonline.com/news/view/20440/linux-operating-system-aimed-at-scientists <![CDATA[Linux operating system aimed at scientists]]> The Bio-Linux operating system is based on Ubuntu 14.04 LTS (Trusty Tahr), and the previous version was using Ubuntu 12.04 LTS. The developers only use LTS releases and that means that upgrades for this distro don't come along all that often.

This Linux distribution is aimed at scientists and it comes with more than 250 bioinformatics packages, 50 graphical applications and several hundred command line tools. And this is just skimming the surface of what the OS can do. Users have access to even more apps from the official repositories.

Bio-Linux is using an Ubuntu LTS version as its base

The fact that it uses Ubuntu LTS versions for the base is a good thing because it means its users won't have to worry about the support. Ubuntu 14.04 LTS is supported until 2019, so people who are using Bio-Linux shouldn't have a problem.

"An updated Bio-Linux 8 version is now on the website in ISO and OVA versions. As usual, there is no need to download this version if you are an existing user. All updates to existing packages will be applied to your system through the update manager and new packages are all available via apt-get or Synaptic," reads the announcement.

The changelog also states that a problem that was preventing the desktop to not start on VirtualBox has been fixed, the QIIME and Bowtie-Bio tools have been upgraded, the pandaseq paired end assembler has been added, and the beginners tutorial specific to Bio-Linux 8 has been improved.

Check out the official announcement for a complete list of changes and updates. You can download Bio-Linux 8.0.5 right now from Softpedia and give it a spin. It has the Unity desktop and now it runs very well in virtual environments.

Reference @ http://news.softpedia.com/news/Bioinformatics-Distro-Bio-Linux-8-0-5-Now-Available-for-Download-469867.shtml

]]> Pranjali Yadav