Andreas Matern › Likes

Ian Simpson
I feel very sorry for him, but this is a very amusing article from the Guardian
Abhishek Tiwari
Do scientists really need a PhD? : Article : Nature -
"Young scientists at a Chinese genomics institute are foregoing conventional postgraduate training for the chance to be part of major scientific initiatives. Is this the way of the future?" - Abhishek Tiwari from Bookmarklet
and you can order that latte with amazing accuracy. - Mickey Schafer
Please delete this post - it could be infectious. All it takes is for a few undergraduates to get wind of this and you could tip over the whole apple cart. - Jeremy Leipzig
Too late, don't tell my PI (Steve Koch) but I'm leaving the lab now. I knew I didn't have to work for free for a chance to be successful! - Anthony Salvagno
with or without a frothy introduction... - Mickey Schafer
Why do mathematicians need PhDs? Discussion from - Mackenzie Cowell
@Mark, another idea before its time: - Steve Koch
@Anthony you said you were going to the library to make photocopies??? - Steve Koch
Mikael Huss
I'd like to extract, for a rather long list of human genes, info on tissues or cell types where they are known to be important in some automated way from literature. Any suggestions for where to start? Extracting Gene Ontology terms will miss many known gene-tissue associations. Is there a text mining tool that can find gene/cell-type associations?
Thanks Neil, AceView is a nice resource that I had forgotten about. I think I can get started by digging there. BioGPS I had already been playing around with. It is also a great resource, but I would like to collect literature mentions of genes in the context of tissue specific activity and/or diseases in addition to expression data. - Mikael Huss
You may want to have a look at HPRD (Human Protein Reference Database) . The database is reporting gene - tissue information based on extensive literature curation. - Khader Shameer
Thanks, Khader, another good suggestion. BTW, is a nifty resource, but it does not seem to provide any kind of downloads. - Mikael Huss
I'm not sure if there are Genetics/Celluar biology professionals on yet, but you might want to try to ask there. - Jane Breezler
Attila Csordas
now is the perfect time to read An introduction to scripting in Ruby for biologists by @jandot & Andy Law
Andrew Perry
Writing a parser in Javascript : Top Down Operator Precedence -
sweet! - Ian Holmes from BuddyFeed
Michael Habib
Fwd: Scholarly Identity 2.0: Matrix, Concept Model, and Presentation - (via (Full description of how these models interact and an overview of the presentation.
Richard Akerman
US, UK, Australia and New Zealand now all have official national-level open data sites.
thank you, where exactly can these be accessed? - Claudia Koltzenburg
Michael Kuhn
Scott Beale
Torfinn Nome
I want to easily annotate, share and compare gene sets with other group members. What is the best tool? I have looked at Gene Set Builder, WebGestalt and Genephony. Have not found exactly what I'm looking for. What do you use?
I have used something less sophisticated GeneVenn earlier, will try other tools you have suggested. Can you elaborate a bit on what you are looking for ? Also Fwd your query to The Life Scientists group. - Khader Shameer
Our group wants a repository of interesting gene sets. With references, comments, tags, etc. Both our own gene sets, and published by others. All gene sets I upload should be automatically available to other group members. Don't need the advanced features of the tools I mentioned. A collaborative version of GeneVenn (thanks!) is what I'm looking for. - Torfinn Nome
Have you looked at NextBio? I would be happy to answer any questions or show you what it can do. Lisa - NextBio
Yeah, Lisa I was checking if such a feature is available with NextBio. If not, you guys can easily incorporate it - right ? - Khader Shameer
We have share and compare tools. As far as adding new features - well, we can build new features pretty easily and we can even build them quickly, but there is a looong list of new features already in the queue and a new feature you request might not get released quickly. We do have APIs. - NextBio
I think API's are available only with NextBio professional license. No donuts for me :( ! - Khader Shameer
Donnie Berkholz
Early Risers Crash Faster Than People Who Stay Up Late: Scientific American -
"An hour and a half after waking, early birds and night owls were equally alert and showed no difference in attention-related brain activity. But after being awake for 10 and a half hours, night owls had grown more alert, performing better on a reaction-time task requiring sustained attention and showing increased activity in brain areas linked to attention. More important, these regions included the suprachiasmatic area, which is home to the body’s circadian clock. This area sends signals to boost alertness as the pressure to sleep mounts. Unlike night owls, early risers didn’t get this late-day lift." - Donnie Berkholz from Bookmarklet
I knew it! - Fossil Huntress
I always secretly knew we night owls were better adapted than those crazy-up-before-dawn people! - Lindsay
Posted at 11:15 pm local time ... and still going strong! - Donnie Berkholz
is SA late to this - that paper came out a few months ago. There was some good coverage of it, e.g., - Bora Zivkovic
For the record, I'm liking this at 12:32 AM Eastern. - Chris Lasher
This reminds me, it's 5:58am here... Off to bed. - Ricardo Vidal from iPod
Glad to see one positive about us night owls. Many are touting the harm of going against circadian cycle. Have been a day sleeper for ten plus years-no harm no foul. - Celt MacGann
I know this feeling... Have had far too many days where my brain only really starts to wake up at 6pm, just in time to leave office because girlfriend/social life/other commitments are calling - Andrew Clegg
This is the most visited post on all of my blogs at all times: Everything You Always Wanted To Know About Sleep (But Were Too Afraid To Ask): Four years old but still pretty much up to date. Explains it all. - Bora Zivkovic early birds get a whole day's work done in that first hour and a - Mary Canady
@Bora spectacular post! Love the wealth of information and dearth of politics :) Feel less guilty and more hopeful already. Here's one of my favorite lines from Bora's post: 'Of course, all of the above are the strategies to shift your clock to a "socially accepted" phase. But you are not crazy or sick. It is the societal pressure to get up at a certain time that is making you sick. Try... more... - Steve Koch
@ Bora -- loved the post, too! I especially appreciated the discussion of light -- I spent a few months reading up on the impact of light, and a Science channel feature on biochronology a few months ago found that very bright light did a lot to help Alzheimer's patients and that planning around an individual's circadian rhythm could ease the side effects of chemo while increasing... more... - Mickey Schafer
That was my first true science post, from January 2005, the one that showed me there is interest in this and I could move from blogging politics to blogging science. I posted it on a brand new blog that nobody knew about, just set up, and the next day it was linked by BoingBoing, Andrew Sullivan and others. Even today, it is still my most visited post ever (and that counts ONLY the... more... - Bora Zivkovic
Deepak Singh
The web as platform: Search as UI -
Another example that comes to mind is using InChi for describing small molecules - as far as I remember the InChi representation was explicitly designed to be search engine friendly (unlike the already established SMILES representation). - Andrew Perry
Brad Chapman
Differential expression analysis with Bioconductor and Python -
Antony Williams
Joel Webber
Drugs in Portugal: Did Decriminalization Work?
"Portugal, which in 2001 became the first European country to officially abolish all criminal penalties for personal possession of drugs, including marijuana, cocaine, heroin and methamphetamine." - Joel Webber
"At the recommendation of a national commission charged with addressing Portugal's drug problem, jail time was replaced with the offer of therapy." - Joel Webber
Wow, I did not know this, and it's great. - Tudor Bosman
"Judging by every metric, decriminalization in Portugal has been a resounding success," says Glenn Greenwald, an attorney, author and fluent Portuguese speaker, who conducted the research. "It has enabled the Portuguese government to manage and control the drug problem far better than virtually every other Western country does." - other countries take note. - Brian Sullivan
There's a bit at the end where a naysayer says something to the effect of ~"this only proves that drug use failed to *increase* under these policies". I read the report differently, but either way it takes some of the wind out of the sails of the "legalized drug use will turn us all into junkies" camp. - Joel Webber
Meant to say this earlier: Vamos na Portugal! - Joel Webber
Pierre Lindenbaum
NCBI Genome Workbench Home Page -
Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results. Genome Workbench is built on the NCBI C++ ToolKit and uses cross-platform APIs for graphics. It runs on your local machine, and is available for Windows 2000/XP, Linux, MacOS X, and various flavors of Unix. Download recent versions from the NCBI Genome Workbench FTP Site , or choose one of the download links below: - Pierre Lindenbaum
That's interesting, anyone using it yet with their own data? - Andreas Matern
Bret Taylor
Human landscapes from above - The Big Picture -
Human landscapes from above - The Big Picture -
Show all
amazing. Makes me want to go out and buy an airplane. - Thomas Hawk
I wonder how far out in advance they have to arrange to take those pictures. All by one photographer from across the globe... - Kevin Kuphal
I just love this kind of photography! Beautiful. - Rachel Lea Fox
luv those pictures, one of best series seen! great job ;) - Dani Martínez
I love the picture of the Maunsell Sea Forts. Looks like it would be fun to visit. - Ross Miller
Andrew Clegg
I'm thinking about putting a proposal to bring our data resources kicking and screaming into the Semantic Web. I'm thinking RDF publishing, Linked Data compliance, microformats, ontological tagging. Has anyone been involved in a project like this? Anyone care to share experiences or ideas?
No huge amounts of experience but starting down that same road as and when we can so would very much like to share the experience and ideas - Cameron Neylon
What do you mean with "our data resources" ? :-) - Pierre Lindenbaum
I work in Christine Orengo's lab at UCL, so primarily CATH and Gene3D, any parts of our internal data warehouse BioMap that might be useful to others, and spin-off projects from these. - Andrew Clegg
First things that come to my mind; describe your projects using the DOAP ontology, your staff using FOAF, create an ontology for your data (e.g. see Eric Jain's work ( on uniprot)( see the NCBO for not re-inventing the wheel), add RDFa to your web pages, make your data available as RDF , etc... - Pierre Lindenbaum
I like the idea of RDFa as a good way to start sneaking semantic markup in without major upheaval, thanks Pierre. DOAP for biological data resources -- interesting -- could maybe do with extending a little - Andrew Clegg
It's still unclear to me what the value of this is today, to the people doing it or anyone else ... could anyone help me out? - Donnie Berkholz
We just put in a proposal to build our data repository, and then publish our data. I would be interested too in hearing others experience. FYI, the Bio2RDF site has some info on how they rdfized their data - - Melanie
@Frank easy integration via common protocol (sparql) with other resources? If I want to access your data I don't need to know about your webservices, or parse your files for example. If I query your database and get a result, I can directly pass it on to the next resource, no need to input it to an other script or website. - Melanie
@Frank - Indeed, the point being that it is easier with RDF. My repository is planned as an Oracle RDBMS, and I am looking into rdfizing my resource, or translating at query time. Some template queries are available at Doing the same querying individual databases would be much more painful. - Melanie
@Donnie something like DOAP allows robots to find your data (and their meaning) - Pierre Lindenbaum
Pierre has an excellent set of suggestions, and let me add one more: Write a detailed account of what you did and problems you faced along the way to make it easier for the next guy to go down that road. - Mr. Gunn
@Frank: If you think SQL is a "common protocol", then you haven't been using more than one RDBMS :-) - Eric Jain
Liked cause this is a fascinating discussion - Deepak Singh
@Gunn yep, that'll be the paper at the end :-) @Frank and Donnie -- you wouldn't want to give Johnny Random access to your RDBMS remotely would you? Even read-only, the ability to run arbitrary queries could bring it to its knees. But with RDF, the raw data is there at a sufficient level of granularity that they can run arbitrary and unlimited queries at their expense across all your data... - Andrew Clegg
... not to mention, mashups of your data with other people's. Plus, I like where this is going and how quickly it's growing: ... and I don't want to continue not being on it - Andrew Clegg
@Mr Gunn : I started to think about how to RDF-ing my data. I'm currently stopped, because I would like to handle those data with some mysterious tools (Taverna, Biomoby, semantic-ws, etc... ) but I still haven't understand how to use them.while I'm sure there is something good to do with them. - Pierre Lindenbaum
@Andrew Ensembl, UCSC and GO allow an anonymous access to their mysql DB. e.g. mysql -N --user=genome -A -D hg18 - Pierre Lindenbaum
Is that entirely sensible? As an occasional DBA and SQL developer I'm well aware that a badly-written query on a large join can be indistinguishable from a DoS attack - Andrew Clegg
Some databases (e.g. Oracle) have detailed options to restrict the resources that can be used per user or query. For databases that use one-process-per-query (e.g. PostgreSQL) you may be able to use OS-level process limits. I'd be interested to hear how Ensembl handles this! - Eric Jain
you can limit the resources of an account - Pierre Lindenbaum
It would still make me nervous. I've worked at organisations where even internal people outside the DW team aren't allowed to execute arbitrary queries. However I've just derailed my own thread so what do I know :-) - Andrew Clegg
In the case of UCSC I think they have a dedicated and isolated mysql server where the data is copied for this external use. - Pierre Lindenbaum
Just so we're not comparing apples to oranges: Direct access to a RDBMS via SQL is comparable to direct access to an RDF database via SPARQL. The data we can get this way (i.e. tab-delimited or RDF data, resp) could be obtained through other channels (e.g. FTP, which is less flexible, but more suitable for large amounts of data). - Eric Jain
I kinda wish I hadn't mentioned query cost as an argument against direct SQL queries. That's actually a side issue. The most important part of RDF publishing seems to me to be the ability to mash up one source of data with another (and another and...) -- breaking down those silo walls and following chains of knowledge across the web - Andrew Clegg
That's why we're all looking for a stable common identifier for our data (remember LSID ?) and that's why you should use an already existing ontology ( ) rather than creating your own vocabulary. - Pierre Lindenbaum
That might be the main argument: SQL (and tab-delimited data, and XML) have no (standard) way to express that some column/value isn't just a string, but represents some concept in another database (which we may even be able to retrieve if we need it and don't have it locally). - Eric Jain
I'm all about the not-reinventing-the-wheel Pierre - Andrew Clegg
If we were able to agree on one central, specialized identifier system and all use the same, non-overlapping vocabularies, RDF might be overkill. Until then, it seems rather useful to have a system that allows us to disambiguate and map our different wheels to each other (and disagree over what ought to be mapped to what). - Eric Jain
One project mentioned on another thread is Okkam(, an EC/FP7 funded project to build infrastructure for an entity naming system. Dunno about others, but personally I find it a bit weird that it has such a low profile online, being a big (?) project. Anybody know more about this? - 'Mummi' Thorisson
"The key objective of the [Okkam] project is to deploy a global and open service called Entity Name System (ENS), which will support the systematic reuse of identifiers for "things" on the Web and generally on the Internet" - 'Mummi' Thorisson
Someone from Elsevier mentioned Okkam in a talk at SESL. I couldn't help thinking that the goal of giving every 'entity' on the web a UID was a bit, well, unachievable. Still, aim high I suppose - Andrew Clegg
To pass on a comment from a mate (who looked into Okkam some more), regarding their low profile: " Since the project is due next year, there's not much time left to involve the community... Amazingly they do offer plenty of tools, like the Word and Protege plugin." - 'Mummi' Thorisson
How did they call the community ? I didn't find any ref on pubmed .... - Pierre Lindenbaum
@Pierre: Their community involvement strategy is all layed out in this password protected document: :-) - Eric Jain
Their website isn't very communicative, but here is a paper that explains the project: Still doesn't make much sense to me though... - Eric Jain
The Shared Names - - project is worth mentioning too. They are meeting next week ( - Melanie
With all those competing projects for centralizing identifiers, you'd think that people would have realized by now how futile this approach is... - Eric Jain
Plus, you can annotate web services with the semantic types they accept and produce (see SAWSDL) so you know any data published with a conforming type will fit. Not sure how many people are actually doing this yet (we're not). But you certainly can't do that sort of thing with direct DB access or table dumps - Andrew Clegg
fantastic discussion :) Might be suitable to also include a link to the article about the 10th anniversary of RDF, as linked on FF by Frank, Abhishek, Yann, Pierre, etc: - Allyson Lister
Yeah, I just downloaded that one, looks like a good intro - Andrew Clegg
FASTA is perfect for people who just need the sequence data (including an identifier and a human-readable label). But it's not advisable to put much more than that in there (some have tried)... - Eric Jain
TAB-delimited data is great for "flat" data such as lists of identifiers. But it won't work well for complex data (data types, references) without a RDBMS-specific schema. Also, once the data has to be split into multiple files, it's no longer practical to process the data without loading it into an RDBMS first. - Eric Jain
TEXT has a lot going for it: It's by far the cheapest solution to work with as it can be edited and displayed directly. But it gets quite ugly as the data gets more structured (natural for a growing database) and code needs to manipulate the structure in more detail rather than just passing around blobs of text. - Eric Jain
XML can get rid of the custom syntax quirks that tend to accumulate in text formats. But we now need to invest quite a lot of effort into creating human-readable/editable views of the data, and shuffling around the data (especially large amounts) is a lot more involved. There are some code generation tools, and to pass around complex data without handling it there is a generic tree data model. XQuery can be used to query within (sets of) documents. - Eric Jain
RDF addresses some of the issues XML leaves open (e.g. how to identify and reference resources globally) and provides a much more useful (for data integration, at least) non-document centric, graph-based data model (plus a standard query language). The "schema" language (OWL) is more focused on describing logical constraints than syntax (as is the case with XSD). - Eric Jain
Note that all of these formats can either be generated on the server-side based on some (more or less standard) query mechanism, or they can be pre-generated and distributed in bulk (e.g. via FTP). So that's really a separate issue. For publishing data, I consider TEXT and XML to be legacy formats (i.e. you might need to continue to support them, but wouldn't bother providing them for new databases). - Eric Jain
The RDF distribution of UniProt was being used in various RDF demonstration projects. Don't know if anyone (outside of UniProt) has started using it (the main part, not just the smaller parts such as the taxonomy) for "real" work since then (i.e. end of 2007). - Eric Jain
Scott Beale
short film featuring inanimate objects from the streets of NYC animated using the voices of interviews with New Yorkers
Paul Buchheit
Have you installed the FriendFeed notifier yet?
The notifier is my favorite new feature in a long time. Try it out and let me know what you think. (it works on OSX, Windows, and Linux, btw) - Paul Buchheit
Yes, it is pretty darn great, especially when you have it focus on a short list of people you really must interact with in almost realtime. With it turned on to too many people, it is an overlapping chore. Thanks for the cool apps! - Josh Haley
I just did. Thanks for the reminder! - Robert Scoble
Wow, this is slick. Turning off gtalk now - Christian Burns
Yes, and <3... wish it was resizeable, though. excellent otherwise. - .LAG liked that
I love it. It's the least intrusive Air App I've seen. I would like the ability to add my comments and likes and a list. That would really make it easier to keep up with conversations. :) - Andrew
LOL@4G RAM. My main laptop has 512MB - Rahsheen
Glen, Air can be a resource hog, but the notifier seems to use less memory that some other Air apps (on my computer, TweetDeck has a 283MB resident size, by the notifier is only 54MB). - Paul Buchheit
air... ick... installed, but not too hopeful - anna sauce
man, i'm wishing i hadn't downloaded. i already have growl notifications and mail notifications ... overwhelmed. - Lynne d Johnson
This tool is usefull, but not my need. I don't like to be disruptted. - pastas9 from BuddyFeed
You can have FF and Twitter on your desktop with one app: Thwirl. And, with Thwirl you can turn off ALL notifications. - Phil Essing from twhirl
Yes, but only works sometimes and when it works, it's updates popups hell. :) - Rui Pereira
@JoshHaley I agree, great for a small subset like coworkers or family, but not for your entire feed. - karl dotter
Ok, a couple thoughts. Once I installed the app I had updates constantly, often one over another so this means #1) I am missing way too much good content, #2) I have a very rich experience on Friendfeed since I seem to want to ignore most Twitter updates but want to click into most FF updates, and #3) if I left this thing on I would get zero work done. This application is too dangerous for me. Sorry guys, i had to turn it off. Good to see you are making the experience flexible for all though. Thanks. - Eric - Final Countdown
Oh and +1 for using Morton's Duran Duran post for the app! - Eric - Final Countdown
The problem I have with AIR is that it wakes up the CPU constantly. air apps + battery life = fail. - mjc
Phil, Thwirl is a full desktop client, which is great if that's what you're looking for. The notifier is just a very simple and lightweight notifier, which makes it very easy to passively keep up with what's happening on FriendFeed in real-time. - Paul Buchheit
I liked Eliza more :p - Rodfather
wish you could disabled comments...otherwise, not bad really not blown away i'm afraid - Zee.
Love that notifier. - Francine Hardaway seems to work best--and less noisily--if you make a list of favorite FF content (people and/or rooms) and set the notifier to that... - .LAG liked that
I keep meaning to ask people what they're going on about a FriendFeed notifier. Installing this as soon as I get home. - Jandy
I use twhirl for FF notifications, works well because I also use it for Twitter when my Tweetdeck api requests run out, and for seesmic - AJ Leon from twhirl
who's running old google deskbar? - John Fu
Yeah I'd love to use it but Air is a resource hog I just can't deal with. - EricaJoy
Another thought, I think the X button on the top right could be bigger. I seem to be accidentally opening liks quite a bit when I'm trying to close the pop up. - Andrew
No, not yet - thank you for the reminder - Susan Beebe
No, I haven't yet, quit nagging. ^_^ - Ron Bailey
I did, and promptly removed it after getting pop-ups every second. - Mathew™ aka Youngblood
My ADD ass wouldn't be able to handle the distraction. - Brad Williamson
I installed it but with Twhirl sending me twitter updates and that popping up it get's really confusing of what's going on. Plus Twhirl works fine for me. - Patrick from twhirl
would be like @_@ - Will Higgins™
Just tried to install it but the link doesn't open anything. Strange (XP w/ Firefox) - Keith - @tsudo
Used compiz to make some adjustment to opacity, gamma values of the friendfeed notifier and now it is as sexy as jaunty native notifier - Zaki Manian
That guy's a rafa benitez clone. Amazing - Martin Liechti from fftogo
Somebody should do one with Silverlight 3 (beta) with out-of-browser -support. That I could try :) - Jemm
Martin, yeah I've noted this before, hehe. :-) - Kol Tregaskes
Yes and I've made some observations and suggestions here: - Kol Tregaskes
Yes, but don't really keep it on. The sheer amount of activity is so high that notifier is a major distraction from whatever I am doing. I only turn it on when I'm browsing FF fulltime. - Parth Awasthi
I need another popup like a hole in my head. - TranceMist
Not really interesting. Friendfeed is getting kinda boring tbh. - Spencer
it's the dreaded ADOBE AIR. avoid it like the plague! :) - zio bodhisattva
Notifier without actual interface=useless to me. - timedalkat from twhirl
Just installed it but notifiers without filtering options = popup hell - MiaD
I like it. It's like the real-time feed without having to take up a whole tab or sidebar. But I could never have it active at work - far too distracting. At home when I can keep an eye down in the corner while doing other things, it's great. - Jandy
I have. And I like it so far - Martin Liechti from fftogo
its great! - Luigi Centenaro
In pop up heaven - how am I supposed to do any work? - Jan Simmonds
不错的小工具,赞 - 阿石
Tried it, liked it but prefer the IM / XMPP interface, that doesn't cost me CPU since I already have a client running, and also gives me more control over the level of distraction. - Robin Barooah
<3 using Twhirl - Patrick from twhirl
Still prefer to use Twhirl for my FriendFeed updates... It has a Me tab and a Friends tab and a Everyone tab and a tab to share stuff. - Patrick from twhirl
My first impression? I "like" much! - Karoli
I tried it and it's fun but I realized that all the real-time-ness I need I get from the real-time view in a separate window without the distraction. - Sam Grover
Andrew Clegg
Semantic Enrichment of the Scientific Literature 2009 (SESL 2009) -- end of the month at the EBI. Looks like the kind of thing some people here would be into -
This looks very interesting. Duncan how are you involved? Anyone else going to attend? I am going to try to get NextBio to send me :) - NextBio
I've just registered - Andrew Clegg
MGH to use genetics to personalize cancer care - The Boston Globe -
Chris Miller
I'm looking for a semi-automatic way to associated genes with pathways/interaction data. Ideally, my scripts dump a gene list out, (either to file, or to an API), and the program shoots back relevant pathways (and maybe enrichment scores). Any suggestions?
I know of DAVID for GO scores, but I'm looking for something that does pathways too, and can handle fairly large volumes of data - Chris Miller
Blast2Go will map your genes to GO terms and then to pathways from KEGG. May be worth a quick look to see if it will do what you want. - Andrew Perry
Does NextBio do anything like this? I think you have to register but maybe that is free - Shirley Wu
GSEA? ( I believe you can download both the program and their curated list of pathways. If I recall the paper right, I think they've chosen a rather odd test statistic, but judging by its citation history, that clearly that hasn't stopped many people from using it... - Andrew Su
Try e.g. Could expand this into and "or" query if you don't have hundreds of genes, but repeating the query for each gene is probably simpler. Add pathway:* or interactor:* to the query to remove matches that don't have either. - Eric Jain
I have done something similar for a set of genes from Drosophila using pathway data from KEGG. After getting pathway information for the list, I calculated enrichment using custom scripts. - Khader Shameer
Yeah, Khader, I could download KEGG or one of the other DBs, but I'm hoping for something off-the-shelf and easy. Thanks for the suggestions, all - I'll start checking them out. - Chris Miller
For interactions, you can use STRING ( and its API ( For pathways, try iPath ( - Michael Kuhn
You could try signing up for a demo account at commercial provider Ingenuity ( - you only get two weeks to crunch your data before you have to resubscribe with a new email account (and lose all your analysis), but it has the best functional annotation and interface I've found so far. - Daniel MacArthur
If you have a UniProt accession or ID for your gene, you can try sending it to my PHOG server, like this: This gives you a report including KEGG sequences and protein-protein interactions of the query sequence and its orthologs and in-species paralogs. If you want CSV, go instead to We... more... - Ruchira S. Datta
DAVID does do pathways (KEGG and Biocarta). You could try ToppGene, which detects enrichment based on a number of features: - Walter Jessen
Khader Shameer
Bioinformatic challenges for the next decade(s) - Journal Article -
The science of bioinformatics has developed in the wake of methods to determine the sequences of the informational macromolecules—DNAs, RNAs and proteins. But in a wider sense, the biological world depends in its every process on the transmission of information, and hence bioinformatics is the fundamental core of biology. We here give a consideration of some of the key problems of bioinformatics in the coming decade, and perhaps longer. - Khader Shameer from Bookmarklet
FreeMat is a free environment for rapid engineering and scientific prototyping and data processing. -
FreeMat is a free environment for rapid engineering and scientific prototyping and data processing.
FreeMat is a free environment for rapid engineering and scientific prototyping and data processing.
This is similar to commercial systems such as MATLAB from Mathworks, and IDL from Research Systems, but is Open Source. FreeMat is available under the GPL license. - sofarsoShawn from Bookmarklet
I've never seen Matlab/Freemat working. Can it be described just as a GUI over 'R' ? - Pierre Lindenbaum
What is the difference to Octave? - joergkurtwegner
@Joerg: It's in the FAQ: "Who said choice was a bad thing?" :-) - Pierre Lindenbaum
@Pierre, right, see also - joergkurtwegner
I don't do a lot of Matlab, but I'm glad to see projects like this going strong. The world needs high-quality, open source Matlabs and Mathematicas. Here's hoping it's as successful as R is some day. - Chris Miller
This is in the standard Ubuntu repository. Just do a sudo apt-get install freemat. - imabonehead
This is pretty neat, has anyone tried this? I'm curious about its performance and numerical accuracy. I know MATLAB is supposed to have some super-special matlab-fu to enhance its performance as well as proprietary algorithms for their PDE solvers -- does this match up? - Benjamin Tseng
Scott Beale
moving my development machine from Vista to OS X
Ross Miller
Egon Willighagen
Ha, not quite chickenwire, but close :) See - Egon Willighagen
there are lots of them: PubChem blames ChemSpider, but this doesn't even load for me: - Michael Kuhn
Jason Calacanis
Matt Damon on Palin... he does make a good case. Dinosaurs... really?
Yeah, because when I ponder how we will deal with the military industrial complex, global terror, religious extremism, free trade and our shift to a service based economy, I wonder "Hey, what does Matt fucking Damon think of this?!". - Peter Ghosh
Damon makes a perfectly commonsensical point: what do we know about Sarah Palin? - jackmason
@Peter I totally agree with you. I don't see any of my comments garnering a Mahalo page and I have just as much expertise in that area as he does. - Kenton
@peter LOL - John Denver
@jackmason I agree 100%, but these points have been made already by many people. I need someone in government to stand up and say this out loud. I want a network other than MS/NBC to point this out. . .repeatedly. And where the hell are the Obama commercials responding to this? - Peter Ghosh
Good point Kenton. Hey Jason, how can I get a Mahalo page? I could rant all day long. Just ask my FF followers :-) - Peter Ghosh
Spot on, Peter...I TIRE of those that somehow attribute astute political observation to celebrities as if they have a special knowledge of politics based solely on the fact that they are well paid to pretend to be someone else in front of an audience or a lens...Don't get me wrong, I dig Matt and his acting skills but his opinion on ANYTHING means exactly dookie to me... - Live4Emma (L4S)
After watching the video, all I can think about is Team America - "Matt Dayyyyymon" - Peter Ghosh
I've read some inane threads on FF lately, but this may be the most inane. You don't have to listen to him JUST BECAUSE he's a celebrity. But celebrity status doesn't necessarily mean he's wrong. Why not actually defend Palin from the very sensible charges Damon's making, rather than trying to discredit him merely on the basis that he acts for a living? - Lon Harris from twhirl
In the same way I don't take my cues on gun control from Ted Nugent I won't take my cues on Plain or anyone else from Matt Damon. What difference is Fred Thompson's view of Palin as compared to Damon's and why is one given more "credibility" than the other? It's got nothing to do with Palin but everything to do with Celebrity Worship and mindless drones who seek celebrity approval for their beliefs. What qualifies Damon more than my Uncle for opinions on anything? - Live4Emma (L4S)
It doesn't make him any more or less qualified to express an opinion because he's a celebrity, but it certainly doesn't disqualify him, like some people would clearly like to do. It's like anything: don't want to hear it, turn the channel, unsubscribe, etc. - Bob M. Montgomery from twhirl
*click*....I wonder what Smokin' Joe Fraiser thinks of Sarah Palin? The former Heavyweight Champion of the World is famous and because he's human, he has the ability to form opinions that I must vote this November is counting on it.... - Live4Emma (L4S)
My favorite Matt Damon quote : ""For a lot of actors, our biggest fear is that we're going to start talking about things we don't fully understand and sound like idiots,...In the long run, I'll do much more good if, when I open my mouth, I have something worth saying." - Keith Smith
@Lon I have no problem with what Matt has said in the video. I'm certainly not going to defend Palin. My point is that there are plenty of people, far more qualified than some actor, that have been saying the same things, yet without the coverage. Why is it such big news when Matt Damon says it? It seems that because (insert famous actor of choice here) says it, it must be right. - Kenton
But, I mean, it makes sense on one level, right? He makes the point in a funny, compelling way, and people already know and like him from the movies. I understand when people mock celebrities for expressing ill-informed opinions about matters, but why the animosity towards a guy who's clearly at least somewhat intelligent making a good argument? - Lon Harris from twhirl
Kenton, because he said it well in an easy to digest format and with good use of humor. - Scoble, Alex Scoble
My favorite on this topic from a year or two ago: "Nobody should give a shit about an actor's opinion on politics." - James Caan - Jeff Quinton
Matt Damon is a tool, but I will defend with my life his right to be a tool... - John Denver
Jeff, why stop there? "Nobody should give a shit about a politician's opinion on politics." - Alex Scoble - Scoble, Alex Scoble
His question isn't a bad one - but it is answered fairly simply. We know that at no point has Palin attempted to legislate creationism into the school system and we know that she has publicly stated that it is not important as part of the curriculum and that she did not consider it a useful litmus test for teachers. Her father was a science teacher who apparently DID believe in evolution. In short, while it would be good to know her views - panic is not warranted. - Soulhuntre
I just watched the video once again, Matt Damon is concerned about everyone's lack of knowledge about Palin. I understand that and if I was an American voting in the election, I'd be concerned about it too(and as a Canadian I'm still worried because the current lunatic running your country has an impact on us whether we like it or not). However, my point is still this; If the AP had done a man-on-the-street and someone had said exactly the same thing, would he/she have gotten their own Mahalo page? - Kenton
Kenton: Mahalo is not "curated" in the sense that we sit around and decide what news is important enough to make pages on. It's "curated" in the sense that we pick the day's most popular topics and then find the best information about them. Many many people are searching for this Matt Damon clip today. You watched it twice yourself and are now engaged in a discussion about it. That's... more... - Lon Harris from twhirl
OK, thanks Lon, I didn't realize that about Mahalo. I don't need to belabour my point here any longer. As for M.D.'s comments; If Palin were to become President and she decided that a book that Robert Scoble hadn't saved to his hard drive should be burned... What are the chances that she'd actually be able to make that happen? I'm asking this in all seriousness as I assume it would be very difficult but don't know U.S. government procedures well enough. - Kenton
And... I assume that the current President believes that dinosaurs existed 4000 years ago (if he knows what a dinosaur is). He hasn't accidentally set off any nukes. - Kenton
I think he's just confused. It's born-again, not Bourne-again. - Siona van Dijk
Apparently he doesn't know how to get to Snopes : - Keith Smith
Apparently, you don't get what he's saying in the video. He wants to ask her those questions to see if it's true or not. The main point being that she's so new to the scene that we don't know anything about her other than these tidbits from the news. That there's no way that anyone can rationally say that she's fit to lead the country based off of what we know of her. - Scoble, Alex Scoble
Oh, OK. What were Obama's, Biden's, and McCain's answers to the 4,000 year old dinosaur thing? I thought it was Internet noise and didn't realize the candidates were being asked such a dire question. - Keith Smith
They've been out in big party politics for so long that we already know the answers to those questions. And none of them purports to be a creationist, something that to a lot of Americans is synonymous with kook. - Scoble, Alex Scoble
duuuh Matt Daaaaaaaaaaahmon.... TEAM America! Duuuh! Howard Zinn brainwashed him. they must of served the good stuff @ Martha's Vinyard - NoahDavidSimon
I'm shocked people are slamming Damon here, he poses thoughtful questions....this video will factor in people's minds...way to go Matt. - timedalkat from twhirl
But...but...he's a Hollywood celebrity! And he was mocked in a mediocre puppet movie! He's clearly not allowed to have independent thoughts, right, gang? Especially if they conflict with our own snap judgments! - Lon Harris from twhirl
I was making fun of Damon before that movie. he is a great actor... so was Brando... both are idiots - NoahDavidSimon
I like Matt. But, in this short interview he proclaims ignorance ("cuz I don't know anything about her.....but it is a disaster"). - Craig Mische
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