Author: Ibrahim El Merehbi

Best Practices for Scientific Computing

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A summary of a very interesting paper on “Best Practices for Scientific Computing” I read a year ago.

Andrea Cirillo's avatarandrea cirillo's blog

I reproduce here below principles from the amazing paper Best Practices for Scientific Computing, published on 2012 by a group of US and UK professors. The main purpose of the paper is to “teach”  good programming habits shared from professional developers to people  that weren’t born developer, and became developers just for professional purposes.

Scientists spend an increasing amount of time building and using software. However, most scientists are never taught how to do this efficiently

Best Practices for Scientific Computing

  1. Write programs for people, not computers.

    1. a program should not require its readers to hold more than a handful of facts in memory at once
    2. names should be consistent, distinctive and meaningful
    3. code style and formatting should be consistent
    4. all aspects of software development should be broken down into tasks roughly an hour long

  2. Automate repetitive tasks.

    1. rely on the computer to repeat tasks
    2. save recent commands in…

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Assorted links – Data Science with R

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last updated: 2015-08-29

References & Most helpful commands

Tutorials & Handy packages

Hands-on dplyr tutorial for faster data manipulation in R Interactive Visualizations From R Using Rcharts rMaps – Interactive Maps from R (github repo) (requires “devtools” from cran)
Using R for Psychological Research – Personality Project, William Revelle
DataCamp courses
Try R by Code School (on codeschool)
Introduction to R, Leada

Visualization Packages

see Assorted links – Data Visualization (to be published later)

Papers

Tidy Data, Hadley Wickham [PDF]

Journals

Big Data & Society – Open-access journal

Hacks for better productivity

Sublime and R

Using Sublime Text 2 for R Using R in Sublime Text 3

Books

Video (training) courses

Introduction to Data Science with R, Garrett Grolemund, O’Reilly Media

Lists of Resources by others

Data Mining

Scraping Twitter and Web Data Using R – Pablo Barbera

Numerical Analysis
Interoperability
Data Sources

see Assorted links – Data sources (To be published later)

If you’d like to contribute to this list, please leave them in the comments below.

Update on the Rosetta (comet) mission

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The Rosetta orbiter is continuing its science until the end of the extended Rosetta mission in September 2016. The lander’s future is less certain. This film covers some of what we’ve learnt from Philae about comet 67P/Churyumov-Gerasimenko so far.

This includes information about the comet’s surface structure from the ROsetta Lander Imaging System – or ROLIS camera – a copy of which can be found at the German Space Agency, DLR, in Berlin.

Data from all Philae’s instruments has informed the work of the other scientific teams. Rosetta scientists have analysed grains from the comet and discovered that it contains carbon rich molecules from the early formation of our solar system.

The video also contains footage from the Max Planck Institute for Solar System Research in Germany – where a flight replica of Philae’s COSAC instrument is maintained in a vacuum chamber to test commands. COSAC has already detected over a dozen molecules containing carbon, hydrogen, nitrogen and oxygen from the dust cloud kicked up from landing.

NASA’s JPL releases Two Math Libraries

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NASA’s Jet Propulsion Laboratory (JPL) has released two large math libraries under an open source (BSD) license. Via Degenerate Conic:

“MATH77 is a library of Fortran 77 subroutines implementing various numerical algorithms. It was developed over decades at JPL, and contains some very high-quality and time-tested code. The code is released under a BSD-type license. There is also a C version for people who love semicolons.”

This goldmine includes basic mathematical functions, random number generators, linear algebra routines, solvers for systems of nonlinear equations, curve fitting, interpolation, and quadrature routines, and much more. The libraries are available at Netlib and are accompanied by 619 pages of detailed documentation.

[via jblevins.org]

Fortran Wiki

Stagefright Android MMS Vulnerability (July 2015)

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A security researcher discovered a vulnerability in the Android MMS system which could be exploited to control Android phones without the user doing anything. It was reported to Google in April and a patch was release.

Unfortunately, as is the case with most manufacturers, the Android system rarely gets more than one or two upgrades.

The vulnerability affects Androids 2.2 to 5.1.1 which is the majority of smartphones currently in use.

To reduce the risk of being exploited you should disable MMS auto-retrieval in you SMS app, Hangouts app, and any other apps that deal with your SMS & MMS. To do this go into the settings of each app and disable MMS auto-retrieval. See the images below as a demonstration as well as the link at the end of the post.

For more on the topic and to stay updated follow the topic on Quora and these threads & articles:

Stagefright Android MMS Vulnerability (July 2015): What is Stagefright Android MMS vulnerability?

How do I protect my Android phone from the Stagefright vulnerability? FAQ

How To: Protect your Android device from the MMS-hack (Stagefright exploit)

Latest news about Stagefright