<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/42497?offset=560 https://bioinformaticsonline.com/blog/view/44766/genome-simulation-with-slim-and-msprime Fri, 31 Jan 2025 12:47:43 -0600 https://bioinformaticsonline.com/blog/view/44766/genome-simulation-with-slim-and-msprime <![CDATA[Genome Simulation with SLiM and msprime]]> Genome simulation is an essential tool in population genetics, enabling researchers to model evolutionary processes and study genetic variation. Two widely used simulation tools in this field are SLiM and msprime. While both serve different purposes, they can be used together with the slendr framework to compare simulation outputs effectively.

Overview of SLiM and msprime

SLiM: Forward Genetic Simulator

SLiM is a free, open-source tool designed for forward genetic simulations. It allows researchers to model complex evolutionary scenarios, including selection, recombination, and demographic events, making it particularly useful for studying adaptation and selection in populations.

Key Features of SLiM:

  • Simulates population evolution forward in time

  • Supports custom evolutionary models using an embedded scripting language

  • Allows modeling of spatial and ecological dynamics

  • Provides high flexibility and extensibility for user-defined scenarios

  • Available on GitHub as an open-source project

msprime: Ancestry and Mutation Simulator

msprime is an efficient, open-source tool that simulates ancestry and mutations using a coalescent framework. It is known for its high-speed performance and low memory requirements, making it a popular choice for large-scale genomic simulations.

Key Features of msprime:

  • Implements coalescent simulations for ancestry modeling

  • Efficiently simulates large population histories

  • Supports the addition of mutations to genealogies

  • Developed using an open-source community model

  • Often faster and more memory-efficient than alternative simulators

Using SLiM and msprime with slendr

Both SLiM and msprime can be integrated with slendr, a framework that facilitates structured population genetic simulations. This integration allows for seamless comparison of simulation outputs.

How They Work Together:

  • SLiM and msprime simulations can be analyzed within slendr.

  • The ts_read() function in slendr enables loading and comparing tree sequence outputs from both simulators.

  • This integration allows researchers to validate simulation results and gain deeper insights into evolutionary processes.

Performance Considerations

While SLiM offers powerful forward simulations with extensive customization, msprime is often preferred for its speed and memory efficiency when simulating ancestry and mutations. The choice between the two depends on the research goals:

  • For detailed evolutionary modeling with selection and recombination: Use SLiM.

  • For large-scale coalescent simulations with mutations: Use msprime.

  • For comparing different simulation models and their outputs: Use slendr to integrate SLiM and msprime results.

Conclusion

SLiM and msprime are valuable tools for genome simulation, each serving distinct but complementary purposes in population genetics research. By leveraging the strengths of both simulators with slendr, researchers can conduct robust and efficient evolutionary simulations, enhancing our understanding of genetic diversity and adaptation.

For more information, check out the official GitHub repositories for SLiM and msprime, and explore the slendr framework for streamlined simulation workflow

]]> BioStar https://bioinformaticsonline.com/pages/view/1130/bioinformatics-courses-around-the-world Fri, 19 Jul 2013 02:43:46 -0500 https://bioinformaticsonline.com/pages/view/1130/bioinformatics-courses-around-the-world <![CDATA[Bioinformatics Courses Around the World]]> Bioinformatics Courses around the world


Here is the list Bioinformatics courses offered around the world. Reasons for constructing this page are:

  1. To show the extent of growth of this new discipline
  2. To provide a resource for students, and academics and
  3. To access notes on the subject to allow some brief comparisons between courses.

The graduate courses outlined in the table mainly exist as a coursework component of an MSc or PhD degree. Of course, many institutions will also have pure research programs in Bioinformatics at the Hons, MSc, or PhD level and will not have a 'coursework component'. These research programs may not always reflect the main research program of the institution since the research depends upon the interests of a particular individual or small team within that institution. It is difficult to track these individual research programs. Consequently, we have not included all institutions with a bioinformatics research project. Bioinformatics is an interdisciplinary subject and this is reflected in the fact that the courses are offered by departments or schools as diverse as: computer science, biochemistry, molecular biology, microbiology, engineering, and mathematics. Similarly, bioinformatics may also be known by other names such as: computational biology, biocomputing, molecular informatics, computational molecular biology, biological information theory, molecular phylogenetics, and molecular bioinformatics.

Bioinformatics University Courses

US

Canada

Europe

UK

Sweden

Norway

Germany

Finland

France

Denmark

Belgium

Switzerland

Austria

Israel

New Zealand

Australia

Asia & South Pacific

Africa


Others:


Advanced Courses and Papers

 

If your university is not there in the list, please let me know info_at_bioinformaticsonline.com

]]> Jitendra Narayan https://bioinformaticsonline.com/opportunity/view/2335/embo-practical-course-bioinformatics-large-scale-data-at-shenzhen-china Wed, 14 Aug 2013 09:50:56 -0500 <![CDATA[EMBO Practical Course, Bioinformatics, large-scale data, at Shenzhen, China]]> This international advanced course will provide training on bioinformatics and statistics methods for genomic research. It will give insight into how biological knowledge can be generated from high-throughput sequencing (DNA-Seq, RNA-seq, ChIP-seq) experiments and will illustrate how to analyze such data. The course covers both the underlying statistical and algorithmic concepts, and the practice of how to automate and code such analyses using the scripting language R.

17 Nov 2013 -22 Nov 2013

More at http://events.embo.org/13-large-scale-data/

Online Registration: https://www.conference-service.com/pc13-47/welcome.cgi

]]> https://bioinformaticsonline.com/pages/view/42809/bioinformatics-in-africa-part2-kenya Sat, 06 Feb 2021 13:23:54 -0600 https://bioinformaticsonline.com/pages/view/42809/bioinformatics-in-africa-part2-kenya <![CDATA[Bioinformatics in Africa: Part2 - Kenya]]> International Livestock Research Institute (ILRI):

Under   a   NEPAD   initiative,   the   Biosciences   Eastern   and   Central   Africa   (BECA)  (www.biosciencesafrica.org) was established at ILRI. BECA consists of a hub, regional nodes, and  other affiliated laboratories and partner institutes. A state of the art joint Bioinformatics Platform  (www.becabioinfo.org), whose overall goal is to provide a coherent and powerful bioinformatics  infrastructure for use by all scientists in East and central Africa. The Platform goal requires both  physical and intellectual developments that together provide researchers with access to diverse  infrastructure in a wide­area network, thereby addressing four important aspects of bioinformatics: 

1) Science: bioinformatics tools for data integration and visualization, standardization of data  formats and data analysis strategies, and distribution of analysis tasks over local­ and widearea networks are in development; 

2)  Bioinformatics Support Facility: provides assistance and custom programming to projects  and those unable to establish a bioinformatics support function intrinsic to their project due  to shortage of qualified personnel or lack of funding; 

3) Hardware Platform: provide a powerful high performance computing platform capable of  handling the largest analysis needs for projects; 

4) Bioinformatics Training for East and central African scientists: While many Web­based  tools are available to the wet­lab researcher, the Web is not well suited for tasks beyond  single­sequence annotation. Researchers need to become productive in a server­based Unix  environment with its wealth of scripting and automation tools. Even at an entry­level, this  can be an intimidating task if proper guidance is not available.

International Centre of Insect Physiology and Ecology (ICIPE): ICIPE’s research focus is on insect biology, in order to improve the wellbeing of the peoples of the  tropics through insect science. There is a commitment to utilise contemporary science in order to  limit the impact of disease vectors, and agricultural pests. The understanding of the mechanisms  associated with behaviour (e.g. attraction and repellency) is crucial. ICIPE seeks to enhance its  bioinformatics capacity in order to support data from various EST projects designed to gain insights  into the insect ecology and plant pathogen interactions though studies of metabolic pathways  associated with production of all elochemicals. 

Long­term training activities:

Kenyatta University: An introductory course in Bioinformatics is offers to MSc Biotechnology  students. This comprises of 35 hours of lectures and practicals.

University of Nairobi: A centre for Biotechnology and Bioinformatics (CEBIB), which will offer  postgraduate training (diplomas, MSc and PhD) in areas of biotechnology and bioinformatics has  recently been launched. Other universities in Kenya, including Egerton, Maseno and the Jomo Kenyatta University of  Agriculture and Technology offer introductory courses to undergraduates in biomedical sciences. In addition, under the BECA platform MSc and PhD fellowships are being made available for  Bioinformatics students. ILRI is forging links with Universities in South Africa and the United  Kingdom to provide access to courses and training material. 

Research Interest and Activities:

The following are the present areas of research interest: 1. EST clustering 2. Genome sequencing and annotation 3. Functional genomics and proteomics (including key tropical pathogens) 4. Structural bioinformatics 5. Development of Bioinformatics Data Management Systems 6. Gene Mining 7. High Throughput Genotyping 8. Microarray data management and analysis 9. Metagenomics 10. Immunoinformatics 11. Host­pathogen interaction 12. High performance computing and grid development 13. Parasite transfection technologies 14. Cell cycle regulation 15. Population genetics 16. Vector genomics 17. Drug, vaccine and diagnostic target discovery

More at Web site and links:

http://www.ilri.cgiar.org/

http://www.icipe.org/    

http://www.uonbi.ac.ke/cebib

]]> BioStar https://bioinformaticsonline.com/pages/view/42815/bioinformatics-in-africa-part7-tunisia Sat, 06 Feb 2021 21:25:09 -0600 https://bioinformaticsonline.com/pages/view/42815/bioinformatics-in-africa-part7-tunisia <![CDATA[Bioinformatics in Africa: Part7 - Tunisia]]> Institut Pasteur de Tunis (IPT):
The IPT is a research institution founded in 1883. IPT is under the supervision of the Ministry of  Health and is part of the Université El Manar of Tunis (Ministry of high Education). The missions  of the institute are: Public Health Laboratory activities (PHL), Research on infectious diseases, and  R/D on vaccines. Research programs are mainly oriented towards local health problems such as  leishmaniais, viral hepatitis, and scorpion venoms. The   group   of   Bioinformatics   and   Modelling   of   the   IPT   is   hosted   by   the  Laboratoire  d’Immunopathologie Vaccinologie et Génétique Moléculaire  (LIVGM), and exists since the  beginning of 2005. Its present research activities include: genome annotation, EST clustering and  modelling of the host/parasite response to Leishmania infection. It consists of two senior scientists,  two PhD students and one MSc student

Centre de Biotechnology de Sfax (CBS):
Bioinformatics activity started at CBS in 2001 with the setting­up of a research and service unit of  bioinformatics. This unit currently includes one senior researcher, one engineer and four Phd  students. Activities include sequence annotation (service) and three research programs: ab initio  prediction of short eukaryote genes, statistical modelling by Bayesian networks approach of signal  transduction pathways and statistical analysis of human sequence variation data (haplotype  reconstruction and linkage disequilibrium). Activities of the Bioinformatics unit could be found at  the website: http://www.cbs.rnrt.tn/ and the research activity report is available under request to  Bioinformatics@cbs.rnrt.tn. Although the computing facilities are good, there is still a need for  trained human resources to strengthen bioinformatics capacities at CBS, particularly in structural  bioinformatics.

Web site and links: http://www.cbs.rnrt.tn

]]> BioStar https://bioinformaticsonline.com/news/view/39606/amity-university-bioinformatics-summer-program-kolkata Tue, 11 Jun 2019 21:27:10 -0500 https://bioinformaticsonline.com/news/view/39606/amity-university-bioinformatics-summer-program-kolkata <![CDATA[Amity University Bioinformatics Summer Program - Kolkata]]> Registrations are now open for the 2019 Summer Bioinformatics Training program at Amity University, Kolkata. The program will focus on introductory topics for life science students. We will review important history, topics and challenges bioinformatics can help address in the context of basic research, discovery and industry.

Read more: https://edu.t-bio.info/amity-university-summer-bioinformatics-program-registrations-are-open/

]]> eliabrodsky https://bioinformaticsonline.com/news/view/1737/perl-in-a-day Sat, 10 Aug 2013 21:14:03 -0500 https://bioinformaticsonline.com/news/view/1737/perl-in-a-day <![CDATA[Perl in a day !!]]> This pdf based tutorial in good resource to understand the basic of Perl in a day

http://ritg.med.harvard.edu/training/perl/RC_Perl_Intro.pdf

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/3965/ruby-and-bioruby-tutorials Mon, 26 Aug 2013 17:18:28 -0500 https://bioinformaticsonline.com/bookmarks/view/3965/ruby-and-bioruby-tutorials <![CDATA[Ruby and BioRuby Tutorials]]> Collections of Ruby and BioRuby learning materials.

BioRuby paper link : http://bioinformatics.oxfordjournals.org/content/26/20/2617.abstract

Address of the bookmark: http://www.codeschool.com/paths/ruby

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/11175/next-generation-sequencingngs-books Fri, 30 May 2014 04:48:04 -0500 https://bioinformaticsonline.com/bookmarks/view/11175/next-generation-sequencingngs-books <![CDATA[Next generation sequencing(NGS) books]]> Employing different technologies, the purpose of NGS platform is to decode the identity or modification on the nucleotides. NGS platforms evolve quickly and capture the main stream.

This bookmark is created to provide NGS online books links.

Address of the bookmark: http://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Print_version

]]> Abhimanyu Singh https://bioinformaticsonline.com/news/view/21312/r-for-microsoft-excel Wed, 18 Feb 2015 00:43:27 -0600 https://bioinformaticsonline.com/news/view/21312/r-for-microsoft-excel <![CDATA[R for Microsoft Excel]]>

If you currently use a spreadsheet like Microsoft Excel for data analysis, you might be interested in taking a look at this tutorial on how to transition from Excel to R by Tony Ojeda. The tutorial explains how to use R functions in place of Excel formulas, including tools like =AVERAGE and =VLOOKUP. For the most part, it uses modern R packages to keep the R code clear and concise.

You'll likely still be using Excel as a data source, though, so you'll also want to check out this guide to importing data from Excel to R from MilanoR.

Reference http://www.r-bloggers.com/an-r-tutorial-for-microsoft-excel-users/

]]> Jitendra Narayan