Samuel Croset

PubMed Watcher - Tailored biomedical literature feed

admin — Fri, 06 Sep 2013 13:55:26 +0000

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It has always been difficult for me to keep track of scientific literature. On one hand, you're meant to read everything that comes out on your topic, on the other hand most of these papers are not directly relevant to you. Even worse, some of the really interesting articles have been published long ago, and it might be difficult for you to find them the traditional way, specially if the article has a low number of citation or is not hype enough.

In order to address this, I created PubMed Watcher, a web app helping you to keep track in a smart way of newly published work. Enjoy and feedback!

EBI Gravity - Angry Birds meets Bioinformatics

admin — Mon, 28 Jan 2013 21:47:12 +0000

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Experiment

Javascript

Useless fun with the physics engine behind Angry Birds: http://box2d.org/

One can trigger a button affecting a part of the home page of the EBI website. The pieces are then draggable around the screen!

Go to the experiment

Renders better on Chrome (thanks to the awesome V8).

Source code available at GitHub.

Credit: Port box2d to JS, jQuery wrapper.

PubMed²

admin — Wed, 12 Dec 2012 21:53:25 +0000

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PubMed is a popular website to query the research literature related to medicine and life science. PubMed² is an experiment exploring new interactive ways to visualise the search results from PubMed on tablets, smart phones and classical computers. The application renders best on Chrome and Firefox and uses the isotope JS library.

How to use: Enter a normal PubMed or Google query, based on keywords.

Find the experiment there: http://pubmed-square.org/

And the code here: https://github.com/loopasam/PubMedSquare

How to install Sun Java 6 on Linux Mint 13

admin — Sun, 21 Oct 2012 17:56:37 +0000

Most of the Linux distribution don't feature any longer the Sun (Oracle) JVM by default, for licensing issues.

If you want to install it in an easy way (adapted from this).

Get and run the installer:

sudo apt-get purge sun-java
mkdir ~/src
cd ~/src
git clone https://github.com/flexiondotorg/oab-java6.git
cd ~/src/oab-java6
sudo ./oab-java.sh

Install Java Sun:

sudo apt-get install sun-java6-plugin sun-java6-jre sun-java6-bin sun-java6-jdk

Set-up to co-exist alongside OpenJDK:

sudo update-alternatives --config java

Just pick the one you prefer the most.

Don't forget to verify:

samuel@samuel-Latitude-E6510 ~ $ which java
/usr/bin/java
samuel@samuel-Latitude-E6510 ~ $ java -version
java version "1.6.0_26"
Java(TM) SE Runtime Environment (build 1.6.0_26-b03)
Java HotSpot(TM) Server VM (build 20.1-b02, mixed mode)

Brain-1.1: biologic ⊆ logic

admin — Wed, 17 Oct 2012 15:55:18 +0000

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I'm pleased to announce the release of Brain, a library for biomedical knowledge manipulation. Brain simplifies the interaction with the OWL-API and is particularly suited for biomedical knowledge representation (OWL 2 EL). Brain can also be used as a in-memory knowledge-base. A important feature of the library is the possibility to integrate biology with description logic (coming itself from set theory).

The site with all you need to know: http://loopasam.github.com/Brain/

(picture from Wikipedia)

How to start a Maven project and hosting it on GitHub only using Eclipse

admin — Thu, 04 Oct 2012 18:54:44 +0000

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Make sure you have installed the following plugins:

http://eclipse.org/m2e/ (Releases: http://download.eclipse.org/technology/m2e/releases)

http://www.eclipse.org/egit/ (Releases: http://download.eclipse.org/egit/updates)

Then in Eclipse:

Create the new Maven project

- Create a new Maven project, located under your "git" folder (mine is "/home/samuel/git").
- The name of the project is determined by the ArtifactId.

Do the first commit

- Right click on the new Maven project, and click on "Team --> share project". Choose "git".
- Tick the box "Use or create repository in parent folder or project".
- Create the repository by clicking on the button.
- Click "finish"

First commit

- Right click on the project and click on "Team --> Commit...".
- Commit all the files and add as message "first commit".

Preparing the online repository

- Go on GitHub.com and create a new repository with the very same name as ArtifactId (cleaner).
- You should then see the typical guidelines, which we are not going to follow because we are doing it on Eclipse.

Adding the origin remote

- Back to Eclipse, look at your Git repositories: "Windows --> Show View --> Git Repositories".
- You should see your new Maven project here as you have committed to it ("first commit").
- Inside the project (still from this view), right click on "Remotes" and click "create Remotes".
- Enter "origin" as Remote name ("configure push"), then press "OK".
- In the URI field, click on "change". Paste in the URI field the location of the repository you have created online on GitHub (git@github.com:loopasam/Demo.git) and then "Finish".
- Then click on "Save and Push". It should run smoothly.
- Kudos, you have set-up the interaction between Maven, GitHub and Eclipse. You're now ready to start the coding!

How to install Sun Java 6 on Linux Mint 13

admin — Thu, 04 Oct 2012 18:32:07 +0000

Tags:

Java

Linux

Most of the Linux distribution don't feature any longer the Sun (Oracle) JVM by default, for licensing issues.

If you want to install it in an easy way (adapted from this).

Get and run the installer:

sudo apt-get purge sun-java
mkdir ~/src
cd ~/src
git clone https://github.com/flexiondotorg/oab-java6.git
cd ~/src/oab-java6
sudo ./oab-java.sh

Install Java Sun:

sudo apt-get install sun-java6-plugin sun-java6-jre sun-java6-bin sun-java6-jdk

Set-up to co-exist alongside OpenJDK:

sudo update-alternatives --config java

Just pick the one you prefer the most.

Don't forget to verify:

samuel@samuel-Latitude-E6510 ~ $ which java
/usr/bin/java
samuel@samuel-Latitude-E6510 ~ $ java -version
java version "1.6.0_26"
Java(TM) SE Runtime Environment (build 1.6.0_26-b03)
Java HotSpot(TM) Server VM (build 20.1-b02, mixed mode)