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Pierre Lindenbaum › Comments

Pierre Lindenbaum
The Wikipedia Template:Infobox_biodatabase is now integrated in DBPedia - http://plindenbaum.blogspot.com/
Pierre, what about dropping the 'bio' bit, so that I/we can use it for chemdatabases too? - Egon Willighagen
Nice idea. I don't know what would be the simplest way to to this. Is it possible to redirect a template ? is it possible to extend a template ? ... - Pierre Lindenbaum
Don't know... of course, I could just start using the templates anyway... - Egon Willighagen
Pierre Lindenbaum
New blog post: A FUSE-based filesystem reproducing the NCBI Taxonomy hierarchy. http://plindenbaum.blogspot.com/2011...
Hahaha... cool! I want my ontologies mounted like this! - Egon Willighagen
yep, GeneOntology was my first idea but as some nodes can have more than one parent, it would have been more difficult to implement. - Pierre Lindenbaum
But I wonder if we can use this API to create some "virtual project folders" : XML->filesystem with symbolic links to the flat files. - Pierre Lindenbaum
Wouldn't that just show files in multiple folders? You could do something fancy with 'symbolic links' if that child has a preferred parent... - Egon Willighagen
yes you're right. - Pierre Lindenbaum
Egon Willighagen
arghh... my head explodes with ideas for future projects...
Always a good problem to have :) - Rajarshi Guha
well, it's blocking making a deadline right now :( - Egon Willighagen
it usually happens the day before the holidays :-) - Pierre Lindenbaum
Deepak Singh
MyGene.Info provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized. A typical use case is to use it to power a web application which requires querying genes and obtaining common gene annotations. For example, MyGene.Info services are used to power BioGPS. - Deepak Singh
Yann Abraham
ralphewig: Here’s a nice list of Ten Anime Films You Should See Before You Die by Tim Maughan. The majority are scfi, and of the 5 on his list I’ve seen I’ve loved them all. I’m going to have to try the remaining half this summer! - http://idratherbebiking.tumblr.com/post...
ralphewig:
  
Here’s a nice list of Ten Anime Films You Should See Before You Die by Tim Maughan. The majority are scfi, and of the 5 on his list I’ve seen I’ve loved them all. I’m going to have to try the remaining half this summer!
OK, Akira was my one and only choice... :-) - Pierre Lindenbaum
Egon Willighagen
Seeking advice: I need a simple platform with OpenID user account support to build a Java web app to run in some cloud. What should I use?
Not sure if I get the question right, but AWS supports OpenID, doesn't it? - Pawel Szczesny
google apps ? - Pierre Lindenbaum
Pawel, no, I want the web app itself to have openID support.. I want to make a social website.. - Egon Willighagen
Google App Engine just hosts an app, not? I still need a simple toolkit so that I don't have to do any stuff for keeping accounts... - Egon Willighagen
Pierre Lindenbaum
I'm writing my talk "Being Bioinformatician 2.0": biostar, twitter, friendfeed, myexperiment, github, linkedin , blogging. Any other idea ?
Mendeley? - Jason Priem
Wikis, comments on either of the above or scholarly articles. - Daniel Mietchen
Daniel &Jason: a draft for my presentation was posted here: http://www.slideshare.net/lindenb... - Pierre Lindenbaum
Academia.edu? - Ross Mounce
looks great to me. I really like that photo of the coffee break :). - Pedro Beltrao
I think some of the first 20 pages may be a bit hard to make sense of without your words, but given that you will probably talk while showing them, this shouldn't be a problem. Tried to find the Friendfeed conversation depicted on Slide 103, but no 2008 entry in http://friendfeed.com/search... . - Daniel Mietchen
Lanyrd? - Egon Willighagen
@ Pierre, merci! - Daniel Mietchen
Pierre Lindenbaum
my profile in "Microsoft Academic Search" http://academic.research.microsoft.com/Author...
pretty poor coverage. only 7 out of 35 pubs for me - Rajarshi Guha
And they only find 25 citations for the Blue Obelisk paper: http://academic.research.micro... - Egon Willighagen
Pierre', but your profile cannot be right either... or? - Egon Willighagen
no, even if I'm not a pubmed-superstar, some papers are missing. - Pierre Lindenbaum
Six of my 44. - Heather
Pierre Lindenbaum
I'm looking for a cartoon published here on friendfeed TLS, a few years ago. On one side we could see some scientists "2.0" having fun and on the other side, the "gray" scientists "1.0" not having fun BUT writing some papers. Any link ? Thanks.
yes! Many thanks Pawel (and Neilfws on twitter) - Pierre Lindenbaum
Pierre Lindenbaum
I'm looking for "Field guide to next-generation DNA sequencers" http://onlinelibrary.wiley.com/journal... DOI: 10.1111/j.1755-0998.2011.03024.x . plindenbaum@yahoo.fr . Many thanks.
Many thanks Egon ! - Pierre Lindenbaum
Attila Csordas
Do you like the term 'rock star scientist'?
not really - Kubke
No, mainly because it's too often bound up with attempts to decide who is a Rock Star of science -- i.e. more elitist competitive type-A crap. - Bill Hooker
no (i hit like by mistake :() - Dan Hagon from Android
you can call me Pierre - Pierre Lindenbaum
NB I hit "like" for Pierre's comment, not the term! - Bill Hooker
Jeff Habig
Anyone with Science Express access? So excited, I just can't wait. http://www.sciencemag.org/content... Please send to jwhabig at gmail.
I'd like have a copy please to davidcastrog@gmail.com Enviado desde mi BlackBerry de Movistar - David Castro from email
Thanks! Enviado desde mi BlackBerry de Movistar - David Castro from email
Thanks, Pierre! - Jeff Habig
Andrew Su
congratulations for your new position. - Pierre Lindenbaum
Pierre Lindenbaum
Analyzing Exome Data with KNIME - http://www.slideshare.net/lindenb...
Analyzing Exome Data with KNIME
So, what's your conclusion? Seeing from your last slide, I seems you suggest bash over knime? - Egon Willighagen
I told people that KNIME is a good & simple software for the scientists wanting to analyze their data without needing a 'tech-guy' (me) close to them. At the end of the talk, my boss asked me if *I* would use knime to analyze my data: I said 'no', the unix command line is far more faster & useful and people should spend a few hours learing it instead of using a gui. - Pierre Lindenbaum
Pierre Lindenbaum
updated my last post with a KML map of my 'followers' http://plindenbaum.blogspot.com/2011...
yes :-) but it's less fun to program :-) - Pierre Lindenbaum
Pierre Lindenbaum
mapping my "following" to KML.
this sounds strangely sci-fi ... ;) - Kaitlin Thaney
How? Whar are you using as resolver? - joergkurtwegner
Mr. Gunn
The half-life of URLs published in Bioinformatics is about 10 years: YOKOFAKUN - http://plindenbaum.blogspot.com/2011...
but just because the URLs no longer work, it doesn't mean the original page isn't archived *somewhere* - Mr. Gunn from Bookmarklet
and if the URLs work, it doesn't mean that the original work is still available and maintained - Pierre Lindenbaum
Nice work! - joergkurtwegner
Mateusz Koryciński
Do you use XML in your daily work? How are you using it? I'm preparing presentation about XML format. I'm mostly interested in use of it in bioinformatics (e.g. some examples).
Thanks a lot! ;) Do you mind if I use some code from your answers in my presentation? - Mateusz Koryciński
no problem. But please, add a link/ref to those threads on biostar. Will you post your presentation somewhere on the web ? - Pierre Lindenbaum
yes we do as a journal publisher, e.g. when registering doi, so if you wish to talk about journals allowing submission of articles in XML this might be one step ahead maybe also in bioinformatics - Claudia Koltzenburg
Unfortunately it must be in Polish since it is presentation for my classes. Of course If I use some code from BioStar, I will link it to right site. - Mateusz Koryciński
Heather
suelibrarian
Has anyone already got a list of all the "social networking for scientists" sites that are around and springing up? I am rapidly losing track but didn't want to reinvent if there is a current one already. #lazyweb
Ummm, someone was working on one but I've lost track of where it was (or who it was!) I'm afraid. Was just thinking this morning that a wiki for this stuff would be useful. Help people find the service that suits them - help us to compare and critique etc. - Cameron Neylon
Many thanks. More than i imagined There were two that got my attention this week. Colwiz and Peer evaluation. Any one evauated them yet? - suelibrarian
Thanks, Pierre, info updated - Mr. Gunn
Pierre Lindenbaum
Mondrian - Interactive Statistical Data Visualization in JAVA - http://www.rosuda.org/Mondria...
via @rvidal : Mondrian is a general purpose statistical data-visualization system. It features outstanding interactive visualization techniques for data of almost any kind, and has particular strengths, compared to other tools, for working with Categorical Data, Geographical Data and LARGE Data. - Pierre Lindenbaum
Pierre Lindenbaum
The what, where, how and why of gene ontology—a primer for bioinformaticians — Brief Bioinform - http://bib.oxfordjournals.org/content...
(via attila) With high-throughput technologies providing vast amounts of data, it has become more important to provide systematic, quality annotations. The Gene Ontology (GO) project is the largest resource for cataloguing gene function. Nonetheless, its use is not yet ubiquitous and is still fraught with pitfalls. In this review, we provide a short primer to the GO for bioinformaticians. We summarize important aspects of the structure of the ontology, describe sources and types of functional annotations, survey measures of GO annotation similarity, review typical uses of GO and discuss other important considerations pertaining to the use of GO in bioinformatics applications. - Pierre Lindenbaum
Pierre Lindenbaum
Scribl is a javascript, Canvas-based library that easily generates biological charts of genomic regions, alignments, and assembly data. It is perfect for dynamically generating charts and reports for the web. Scribl can also be used in conventional offline pipelines, since everything needed to generate charts can be contained in a single html file. - Pierre Lindenbaum
Pierre Lindenbaum
Dr Dobbs - Full-Text Searching & the Burrows-Wheeler Transform - http://www.drdobbs.com/archite...
Here's an indexing method that lets you find any character sequence in the source text using a structure that can fit the entire source text and index into less space than the text alone - Pierre Lindenbaum
Pierre Lindenbaum
Int3ractive: AS3 Wordle Tag Cloud - http://int3ractive.blogspot.com/2011...
someone who ported my java code (tag cloud) to flash - Pierre Lindenbaum
Pierre Lindenbaum
SeqWare Query Engine: storing and searching sequence data in the cloud - http://www.ncbi.nlm.nih.gov/pmc...
(via Attila) Since the introduction of next-generation DNA sequencers the rapid increase in sequencer throughput, and associated drop in costs, has resulted in more than a dozen human genomes being resequenced over the last few years. These efforts are merely a prelude for a future in which genome resequencing will be commonplace for both biomedical research and clinical applications. The dramatic increase in sequencer output strains all facets of computational infrastructure, especially databases and query interfaces. The advent of cloud computing, and a variety of powerful tools designed to process petascale datasets, provide a compelling solution to these ever increasing demands. - Pierre Lindenbaum
Pierre Lindenbaum
Genome.gov | A Decade with the Human Genome Sequence: Agenda - http://www.genome.gov/27542740
A Decade with the Human Genome Sequence: Charting a Course for Genomic Medicine Ruth L. Kirschstein Auditorium National Institutes of Health Friday, February 11, 2011 8:30 a.m. to 5:00 p.m. - Pierre Lindenbaum
Pierre Lindenbaum
Pierre Lindenbaum
Emerald | Journal of Workplace Learning | Learning to be a programmer in a complex organization: A case study on practice-based learning during the onboarding process at Google - http://www.emeraldinsight.com/journal...
Purpose – This paper seeks to analyse the effectiveness and impact of how Google currently trains its new software engineers (“Nooglers”) to become productive in the software engineering community. The research focuses on the institutions and support for practice-based learning and cognitive apprenticeship in the Google environment. - Pierre Lindenbaum
Pierre Lindenbaum
Genome.gov | DNA Sequencing Costs - http://www.genome.gov/sequenc...
DNA Sequencing Costs Data from the NHGRI Large-Scale Genome Sequencing Program - Pierre Lindenbaum
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