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Best of Bioinformatics
Selected pieces from all areas of Bioinformatics with a kink towards educational topics.
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Why Model? Joshua M. Epstein

Why Model? Joshua M. Epstein | Best of Bioinformatics | Scoop.it

This lecture treats some enduring misconceptions about modeling. One of these is that the goal is always prediction. The lecture distinguishes between explanation and prediction as modeling goals, and offers sixteen reasons other than prediction to build a model. It also challenges the common assumption that scientific theories arise from and 'summarize' data, when often, theories precede and guide data collection; without theory, in other words, it is not clear what data to collect. Among other things, it also argues that the modeling enterprise enforces habits of mind essential to freedom. It is based on the author's 2008 Bastille Day keynote address to the Second World Congress on Social Simulation, George Mason University, and earlier addresses at the Institute of Medicine, the University of Michigan, and the Santa Fe Institute.


Via Bernard Ryefield, Costas Bouyioukos, Pedro Fernandes
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António F Fonseca's curator insight, March 23, 2014 5:20 AM

The classical paper about modelling and simulation. Very clear.

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Stateless Mindset

By Leo Babauta
In programming, there is the concept of statelessness. It means that each request is treated anew, without memory of previous requests.
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PLOS Computational Biology: Education in Computational Biology Today and Tomorrow

PLOS Computational Biology: Education in Computational Biology Today and Tomorrow | Best of Bioinformatics | Scoop.it
PLOS Computational Biology is an open-access

Via Pedro Fernandes
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Dmitry Alexeev's curator insight, December 19, 2013 1:45 AM

A comprehensive description of community effort as well as links to study cources in R and python - very useful for teachers

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Bioinformatics education on Raspberry Pi

Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration.

Via Chris Kelly
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Ed Rybicki's comment, August 20, 2013 4:20 AM
Hate to tell you, but already scooped by Chad Smithson!
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10 Free jQuery eBooks For Programmers

10 Free jQuery eBooks For Programmers | Best of Bioinformatics | Scoop.it
EFYTimes.com presents top free jQuery ebooks along with download links.

Via Pedro Fernandes
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Pedro Fernandes's curator insight, November 30, 2013 9:59 AM

Thanks to Farah Benani for the link.

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Collection of published “guides” for bioinformaticians | opiniomics

Collection of published “guides” for bioinformaticians | opiniomics | Best of Bioinformatics | Scoop.it
(2011) Ten Simple Rules for Developing a Short Bioinformatics Training Course. PLoS Comput Biol 7(10): e1002245. [link]; Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, ...

Via Pedro Fernandes
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Linux Command Line Tutorial

Linux Command Line Tutorial | Best of Bioinformatics | Scoop.it

 

In this tutorial you can learn the basics of Unix using the command line. This tutorial is for you if you have no previous experience with Unix-like systems, or know a few commands but would like to know more.

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Program-Publish-Prove

Program-Publish-Prove | Best of Bioinformatics | Scoop.it

Over the last 10 years, Agile methodologies have been constantly growing in popularity. Today, many developers use Agile best practices on an everyday basis: User Stories, Test- Driven-Development, and frameworks like Scrum.

Now, leading developers claim that Agile methodologies are being over-used in a way that is not Agile any more. The alternative is a scientific development model: Program - Publish - Prove.

 

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Codility. Automated tests of programming skills

Codility. Automated tests of programming skills | Best of Bioinformatics | Scoop.it
Codility saves time of software talent recruiters by filtering out job candidates who cannot write correct programs. Use our automated tool for assessment of programming skills and check if your software developers and coders skills are rock solid.
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ROSALIND - learning bioinformatics through problem solving

ROSALIND - learning bioinformatics through problem solving | Best of Bioinformatics | Scoop.it

Rosalind offers an array of stimulating problems that grow in biological and computational complexity; each problem is checked automatically, so that the only resource required to learn bioinformatics is an internet connection.

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GTPB - the Gulbenkian Training Programme in Bioinformatics - since 1999

GTPB - the Gulbenkian Training Programme in Bioinformatics -  since 1999 | Best of Bioinformatics | Scoop.it

 IB13F - Introductory Bioinformatics.

Feb 25th -Mar 1st

Deadline: Feb 20th

 

 

Please check  the GTPB website http://gtpb.igc.gulbenkian.pt   regularly


Via Pedro Fernandes
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Pedro Fernandes's curator insight, February 11, 2013 11:09 AM

http://gtpb.igc.gulbenkian.pt/bicourses/IB13F/

This is an introductory course in sequence analysis. The pre-requisites are minimal. Participants will learn about what they can do with sequence data using Bioinformatics tools, mostly with open source software, but not only.

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How to use videos to support a training session?

How to use videos to support a training session? | Best of Bioinformatics | Scoop.it

A couple of months ago, Pedro Fernandes suggested spicing up a training session by showing a brief video clip at the beginning. Since then, I have been using videos in several training scenarios. In this article, you find three scenarios described.

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PLOS Computational Biology: Education--

PLOS Computational Biology: Education-- | Best of Bioinformatics | Scoop.it

Recognizing the need for training and education in bioinformatics and computational biology specifically targeted to biologists, PLOS Computational Biology launched its Education section in January 2006. The goals are to provide practical tutorials and background information on important computational methods used to investigate key biological questions as well as resources for training scientists at all stages of their careers. New articles are added to the Education collection as they are published.

Collection URL: www.ploscollections.org/compbioleducation

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▶ RG Group - debugging

RG Group - debugging Enjoy it! We're up all night for debugging. This video was created for the CRG Dance-your-lab Christmas 2013 competition.

Kristian Rother's insight:

Woohoo!

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How Not To Be A Bioinformatician

Although published material exists about the skills required for a successful bioinformatics career, strangely enough no work to date has addressed the matter of how to excel at not being a bioinformatician.
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10 Websites To Learn Coding Interactively

10 Websites To Learn Coding Interactively | Best of Bioinformatics | Scoop.it
Forget complicated setups and cold command prompts, which can force you to quit before you start, here are 10 fun websites with interactive lessons to teach you programming languages!

Via Pedro Fernandes
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Pedro Fernandes's curator insight, November 30, 2013 10:02 AM

Thanks to Farah Benani for the link.

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Why Are There So Many Pythons?

Why Are There So Many Pythons? | Best of Bioinformatics | Scoop.it
Is Python interpreted or compiled? Are CPython and Cython the same thing? And what on Earth is PyPy? Understand the alphabet of Pythons, from start to finish.
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PubMed graphical interface search with new MedLine app

PubMed graphical interface search with new MedLine app | Best of Bioinformatics | Scoop.it
A review of the MEDLINE from Unbound Medicine which offers a revolutionary new way to view medical literature search results

Via Mariano Fernandez S., Pedro Fernandes
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GOBLET - Global Organisation for Bioinformatics Learning, Education and Training

GOBLET - Global Organisation for Bioinformatics Learning, Education and Training | Best of Bioinformatics | Scoop.it

Under the auspices of EMBnet, leaders of a number of International Societies, Networks and Organisations met to discuss world-wide bioinformatics training initiatives. The participants concluded that a Global Organisation for Bioinformatics Learning, Education and Training (GOBLET) is needed to coordinate world-wide bioinformatics training activities: to share, not duplicate, effort; to share, not duplicate, cost; to work together in a mutually respectful way towards common solutions and a sustainable future.

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Why is Creativity Important in Education? Sir Ken Robinson Video Series from Adobe Education

Esteemed education advocate Sir Ken Robinson explains in this short video why creativity is crucial in education, and why it will require a transformation in the way schools work. In his words, “Creativity is not an option, it’s an absolute necessity.”


Via Ricard Garcia, juandoming, Pedro Fernandes
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Ricard Garcia's curator insight, January 14, 2013 2:53 AM

Why don't they pay attention to what he says instead of that continuous void applause?

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Do You Speak DNA?

Do You Speak DNA? | Best of Bioinformatics | Scoop.it

by Mathias Galle

 

“In [these huge molecules] all the wealth and variety of heredity transmissions can find expression just as all the words and concepts of all languages can find expression in twenty-four to thirty letters of the alphabet”. When Friedrich Miescher wrote this in 1892 these words were just speculative as he was not aware of the hereditary functions of DNA, even if he was the first to identify and isolate nucleic acids.

Kristian Rother's insight:

Winning article in the 2011 writing contest on bioinformatyk.eu

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