GenMAPP GSoC Blogs

	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]
	The relation between Garbage bags and Databases Jan 1, 2010 \| Author: Martijn van Iersel \| Source: Helixsoft In my local supermarket, you can find two brands of garbage bags: There are the “A-brand” garbage bags, and there are the “house-brand” garbage bags. Both come in rolls of 20, each bag holds 60 liters, and both come with the same conven ... [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]
	PathVisio 2 released Oct 18, 2009 \| Author: Martijn van Iersel \| Source: Helixsoft This week we released version 2.0 of PathVisio. There has been over a year of active development since the last major release, and a ton of new features. What is PathVisio? PathVisio is a tool for biological pathways. Stay organized! U ... [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]
	Fixing a Pathway the Groovy Way Aug 25, 2009 \| Author: Martijn van Iersel \| Source: Helixsoft It’s no secret that there are many mistakes in WikiPathways. A coworker notified me of a problem with the Focal Adhesion pathway. It’s exactly the sort of problem that requires a lot of repetitive action to be fixed. So I thought, inste ... [read more]
	The “Why” of the Identifier Mapping Problem Aug 11, 2009 \| Author: Martijn van Iersel \| Source: Helixsoft I wrote before about my current work on identifier mapping. Briefly, each of the many different databases for genes and metabolites uses its own system of identifiers. This creates big headaches when you want to compare things from diff ... [read more]
	Mining biological pathways using WikiPathways web services Aug 6, 2009 \| Author: Martijn van Iersel \| Source: Helixsoft A website lets people interact with computers over the Internet. A web service on the other hand, lets computers interact with computers over the Internet. We’ve created a web service for WikiPathways so people can write computer script ... [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]
	Martijn’s Continuous Build System part 2 Jul 19, 2009 \| Author: Martijn van Iersel \| Source: Helixsoft In part 1, I described what a continuous build system is, and what it is useful for. Now I’m going to write about another important use of the build system: testing interfaces between modules. In a modular system, the parts evolve ind ... [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 = Object ... [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 a ... [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 ... [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 D ... [read more]
	GSOC 2009 May 3, 2009 \| Author: Chetan \| Source: Techriti Yeah ... long time since my last post..... What brings me back to blogging is GSOC. I got selected for Google Summer of Code 2009 :). I am one of the 9 lucky ones from my college who made it ( 101 selections in all from India ) . [read more]
	Memo on ID mapping and bridgedb (skyped with Martijn 04/30/09) May 1, 2009 \| Author: JJ Gao \| Source: JJ's blog on bioinformatics ID mapper API needs to be redesigned, using bridgedb Xref. ID mapper API should be generic, or independent of Cytoscape.ID mapper API design V3 on the project wiki is preferred.IDMapperRDB in ID mapping API would be a wrapped-up interf ... [read more]