GenMAPP GSoC Blogs

	Oracle versus Google Aug 20, 2010 \| Author: Martijn van Iersel \| Source: Helixsoft A while back I wrote rather optimistically that I expected Oracle to play nice with the open source community “I don’t see why Oracle won’t be able to keep MySQL open and still have a nice profitable business model.” However, all that ... [read more]
	IT Cooking 1.0 for Android Aug 10, 2010 \| Author: ademcan \| Source: Ademcan’s blog Last year I participated to a challenge organised by Archos. Archos is a french high technology brand and they are creating touchscreen tablets with different screen sizes. Recently they decided to use the Android platform (mobile Oper ... [read more]
	Bio-Informatics.tk Aug 10, 2010 \| Author: ademcan \| Source: Ademcan’s blog FYI I am going to continue writing for my blog using a new address http://www.bio-informatics.tk I will post information related to my work as scientific developer and about Bio-Informatics in general. Keep reading… [read more]
	Going to COMBINE 2010 Jul 31, 2010 \| Author: Martijn van Iersel \| Source: Helixsoft COMBINE 2010 is a meeting about all systems biology standards: SBML, SBGN, BioPAX, … etc. It’s from October 6 to 9 in Edinburgh, just before the ICSB conference. Registration just opened, I’ve already signed up. [read more]
	SBGN 5.5 Hackathon writeup Apr 25, 2010 \| Author: Martijn van Iersel \| Source: Helixsoft The goal of Systems Biology Graphical Notation or SBGN is to define a set of standard shapes for things like reactions, enzymes, genes, metabolites, compartments etc. For example, here is the reaction that takes place in your body after ... [read more]
	WikiPathways Curation Jamboree Evaluation Apr 16, 2010 \| Author: Martijn van Iersel \| Source: Helixsoft WikiPathways content is growing nicely, but it’s not growing like one of those nice exponential curves that you see in the first slide of almost every bioinformatics presentation nowadays. We want exponential curves in our presentations ... [read more]
	That’s Great, Now Please Fix OpenOffice.org Apr 8, 2010 \| Author: Martijn van Iersel \| Source: Helixsoft Did you hear about the OpenOffice.org mouse? It’s a mouse that has no less than 18 buttons. From the press release: “With a revolutionary and patented design featuring 18 buttons, an analog joystick, and support for as many as 52 key c ... [read more]
	BridgeDb: now also with metabolite identifier mapping Mar 25, 2010 \| Author: Martijn van Iersel \| Source: Helixsoft Ha, fooled ya! BridgeDb has been able to deal with metabolite identifiers since the beginning. But mapping genes is such a common problem that metabolites aren’t getting any attention. Nearly all the code examples that we have thus far ... [read more]
	Google Summer of Code 2010 Mar 18, 2010 \| Author: Martijn van Iersel \| Source: Helixsoft Yay! It’s official, we’re going to be in the Google Summer of Code again this year. Our application as a mentoring organization was just accepted. Cytoscape, PathVisio, WikiPathways and even BridgeDb are all joined under the GenMAPP umb ... [read more]
	The Downside of Modularity Mar 13, 2010 \| Author: Martijn van Iersel \| Source: Helixsoft I’m a big fan of modularity. I’ve even got a modular system in my living room. It consists of the following modules: [read more]
	How to develop Modular Software Mar 6, 2010 \| Author: Martijn van Iersel \| Source: Helixsoft It’s always good to make software modular. Modular software is strong and healthy, monolithic software is sickly and bedridden. I’ve touched before on how modularity increases adaptability. But modularity also helps to keep software sma ... [read more]
	Software Carpentry Jan 21, 2010 \| Author: AlexanderPico \| Source: Next Nucleus Yes, even scientists struggle with computer proficiency! [read more]
	BridgeDb paper published Jan 12, 2010 \| Author: Martijn van Iersel \| Source: Helixsoft I’m very happy that our paper on BridgeDb was accepted by BMC Bioinformatics. It’s open access so download it to your hearts content. BridgeDb is all about identifier mapping, which I blogged about before (here, here and here). BridgeD ... [read more]
	Windows 7 Ubuntu like Multi-desktop Dec 1, 2009 \| Author: P.J. \| Source: GeekMi Windows 7 didn't provide multiple virtual desktops as expected. A Solution for Ubuntu like multi desktop is to use 3rd party extensions. It's not perfect, but it's working. [read more]
	The Archaeology of Innovation Nov 19, 2009 \| Author: AlexanderPico \| Source: Next Nucleus In yet another mind-blowing seminar at the Long Now Foundation, Professor Sander E. van der Leeuw condensed millions of years of biological evolution, the archaeology of tools, cities and empires, and revolutions of innovation intoa cog ... [read more]
	RDP on windows over ssh Nov 17, 2009 \| Author: P.J. \| Source: GeekMi First of all, you need to bind the port. Usually we use putty on a windows machine, or ssh on linux. [read more]
	Writing a Book Collaboratively (and Quick) Oct 30, 2009 \| Author: AlexanderPico \| Source: Next Nucleus Put 8 people in a room for 48 hours and produce an 89 page (18,000 word) document! It's called a Book Sprint. [read more]
	Humanity of the Scientist Oct 11, 2009 \| Author: AlexanderPico \| Source: Next Nucleus I'm going to start a list of topics that would constitute the outline for a "humanities for scientists" course. Who knows? Maybe I'll even teach it someday! [read more]
	Article on Java modularity Oct 1, 2009 \| Author: P.J. \| Source: GeekMi Java 7 is out. Here's a good article explains some of the nice features. [read more]
	End of Year Report: GSoC 2009 Sep 9, 2009 \| Author: AlexanderPico \| Source: Next Nucleus It takes a special type of student to succeed in this field and we found 9 of them this summer! [read more]
	Spring Embedded Layout for BioPAX in PathVisio Aug 5, 2009 \| Author: ademcan \| Source: Ademcan’s blog The import part of my plug-in is now working correctly, that means it is possible to open a BioPAX Level3 file in PathVisio. So we can say : ” PathVisio : The first application which can provide you a graphical presentation of a BioPAX ... [read more]
	Conversion from Biopax To Gpml Jun 16, 2009 \| Author: ademcan \| Source: Ademcan’s blog The first part of my plug-in present some results I can open a Biopax file (.owl) in PathVisio. The important conversions from Biopax To Gpml are : - conversion = ObjectType.LINE - control = ObjectType.LINE - physicalEntity = ObjectType ... [read more]
	Google n GSoC \m/ Jun 6, 2009 \| Author: Chetan \| Source: Techriti Y'day, I received my package from Google containing the prepaid Debit card with 505 $ , stickers and a little diary :). [read more]
	First prototype ! Jun 3, 2009 \| Author: Chetan \| Source: Techriti Well a lot of things have happened since the last post. [read more]
	GSEAOK May 27, 2009 \| Author: ademcan \| Source: Ademcan’s blog Today I “finished” (we never finish ) the implementation of the GSEA plug-in for PathVisio. The user have to choose a dataset expression (.pgex file) and a pathway (.gpml file) define the samples to use and the number of permutation and ... [read more]
	Personal Genomics May 22, 2009 \| Author: JJ Gao \| Source: JJ's blog on bioinformatics Some one asked me what was the biggest impression on RECOMB2009. Well, the biggest impression was the desert with a lot of rain--it kept raining for two days. Ooh.. you mean my impression on the conference. That was, the game of perso ... [read more]
	Exams over May 16, 2009 \| Author: Chetan \| Source: Techriti My exams (and my first year of college) got over a few days back. I have spent the last few days packing up and finishing a project which I couldn't complete before. Finally, I got back home today. [read more]
	Biopax and then GSEA… que pasa ? May 11, 2009 \| Author: ademcan \| Source: Ademcan’s blog To be informed… Why changed I suddenly my project working ? You know that I will work on Biopax plugin for PathVisio during the Google Summer Of Code 2009, but coding will start on May 23, so I decided to work on an other interesting pr ... [read more]
	Data Analyst Job May 10, 2009 \| Author: P.J. \| Source: GeekMi Description Description: [read more]
	GSEA : Gene Set Enrichment Analysis May 8, 2009 \| Author: ademcan \| Source: Ademcan’s blog I am actually working on Gene Set Enrichment Analysis. This is a method to determine whether a set of genes shows statistically significant. For example if you have two biological states (cancer and normal) and you have an Expression Da ... [read more]