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Andrew Su › Likes
Top 10 Amazing Biology Videos : http://www.wired.com/wiredsc...
Yaroslav Nikolaev, Jean-Claude Bradley, Andrew Su and 3 other people liked this
STITCH 2: an interaction network database for small molecules and proteins - http://www.citeulike.org/user...
Pawel Szczesny, Yann Abraham, Pedro Beltrao and 3 other people liked this
Nucl. Acids Res. (6 November 2009), gkp937. Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing. To create a network of interactions, STITCH aims to integrate the data dispersed over the literature and various databases of biological pathways, drug-target relationships and binding affinities. In STITCH 2, the number of relevant interactions is increased by incorporation of BindingDB, PharmGKB and the Comparative Toxicogenomics Database. The resulting network can be explored interactively or used as the basis for large-scale analyses. To facilitate links to other chemical databases, we adopt InChIKeys that allow identification of chemicals with a short, checksum-like string. STITCH 2.0 connects proteins from 630 organisms to over 74 000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/. 10.1093/nar/gkp937 Michael Kuhn, Damian Szklarczyk, Andrea Franceschini,...
- Neil Saunders
I didn't expect the paper to come out this quickly, I was quite surprised to see it in my feed reader on the weekend. I have now activated STITCH 2 as public website ... hope it's not too buggy :)
- Michael Kuhn
this looks like it could be quite useful for our cheminfo retrieval class - I added it to our resources and will let you know if any students make use of it for their term projects http://getcheminfo.wikispaces.com/resourc...
- Jean-Claude Bradley
umm .. you are going to make me re-do some work :p
- Pedro Beltrao
@Michael - quick questions: I don't think I ever saw homology evidences in the drug-gene interactions. Do you guys avoid doing this or it is just not reported in the evidence info ?
- Pedro Beltrao
Congrats Michael!
- Ruchira S. Datta
@Pedro: going from STITCH 1 to 2 will change the identifiers of proteins and chemicals, so check first if you run into trouble there
- Michael Kuhn
re transfer: if you are in human or mouse, you probably won't see so much transfer. but if you go to e.g. chimp, you'll see a lot of transferred evidence
- Michael Kuhn
GEO and ArrayExpress agree to exchange UHTS sequencing data. - http://www.ebi.ac.uk/microar...
Andrew Su liked this
Zzzoot: The Future of Science: Semantic Web Applications in Scientific Discourse - http://zzzoot.blogspot.com/2009...
François Dongier, Andrew Su, Yaroslav Nikolaev and 8 other people liked this
"For those who want to take a glimpse at where science and scientific discourse are going, take a look at some of the papers at this workshop"
- Bill Hooker
from Bookmarklet
several of the links are broken - this is the correct link to the Mons slides http://esw.w3.org/topic...
- Jean-Claude Bradley
7 Visualization Groups On Flickr to Find Inspiration - http://flowingdata.com/2009...
Andrew Perry, Chris Lasher and Andrew Su liked this
PathVisio / WikiPathways tool for creating and analysing biological pathway diagrams - http://www.pathvisio.org/
Ami Iida, Holly Rae, FFer, Daniel Mietchen and 8 other people liked this
I'd really like to see that refactored as a collaborative Google Wave gadget.
- Dan Hagon
Me too, re: Google Wave gadget. Then add SBML support, use SBGN in the display, support MIRIAM annotations and I can retire penniless.
- Neil Swainston
@Neil, there are a few other tools which support SBML and SBGN (see http://sbgn.org/Communi...). Wikipathways seem to be inventing yet another pathway format and dont provide a conversion to any other existing "standard". Shame as it would benefit everyone if they did.
- Frank
Thinking about it a little more, I'd really like to see the above refactored as a collaborative Google Wave Gadget. I've been involved in about five network reconstruction "jamborees" now, which involve flying loads of people around the World to sit in a room and discuss things that they could do with PathVisio (if it supported SBML...) or Payao. Anyways, this costs a fortune (see the...
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- Neil Swainston
@Neil: WikiPathways is intended exactly for that type of collaborative pathway creation. WikiPathways pathway format is based on, and developed in cooperation with, http://www.genmapp.org. So admittedly it's not a widely supported standard, but at least it wasn't a complete new invention. SBML / SBGN support is on its way. Re Google Wave: unfortunately, all this work predated Google Wave by several years...
- Martijn van Iersel
Predicting new molecular targets for known drugs - http://www.nature.com/nature...
Ed Millard, Khader Shameer, Matthew Todd and 10 other people liked this
The title is a bit generic, isn't this what Phil Bourne's been doing?
- Ruchira S. Datta
I think this is an extension of their (Kieser et al) previous work with SEA
- Rajarshi Guha
Nature has a story on this in their news section: http://www.nature.com/news...
- Michael Kuhn
Is this using Lasso or similar program? Interesting appearance of DMT as a molecule of interest - I have a student doing a report on it this term http://getcheminfo.wikispaces.com/Adam+My...
- Jean-Claude Bradley
Uses SEA http://sea.bkslab.org/
- Rajarshi Guha
Thanks Rajarshi - looks like another cool online resource to explore
- Jean-Claude Bradley
That's cool. How likely is the top match to be a real inhibitor?
- Andrew Lang
We're trying to run our virtual library of Ugi products we can make in my lab http://usefulchem.wikispaces.com/UClib00... I hope that isn't too large a task
- Jean-Claude Bradley
We did some of this validated cross-target prediction also http://www.nature.com/doifind...
- Matthew Todd
That's awesome Mat! What would be the next step to processing our Ugi product library on the TDI kernel?
- Jean-Claude Bradley
Cool! The WormBase paper for the 2010 NAR Database issue was selected as a Featured Paper!
Frank, Andrew Su, Michael Kuhn and 2 other people liked this
All three manuscripts submitted for the 2010 NAR database issue have now been accepted. Happy days :-)
Hari, Mike Chelen, Peter Miller and 4 other people liked this
Oh bother - talking to NAR about writing something on data licensing was on my list of things to do from last year. Guess I missed the boat again :-(
- Cameron Neylon
Cameron: don't worry, data licensing will not stop being in need of explanation any time soon ;D
- Mike Chelen
Why thankyou Mike, you really know how to brighten my day up...
- Cameron Neylon
A destination list map: RT @brianshiro: fascinating infographic showing the world's most remote places: http://www.fastcompany.com/blog...
Mike Chelen, Rajarshi Guha and Andrew Su liked this
RT @ google Contextual search within Wikipedia: Check out the Google Custom Search Wikipedia skin http://googleblog.blogspot.com/2009...
Andrew Su liked this
@chrisbaglieri my couchDB slides here: http://www.slideshare.net/delagoy...
Deepak Singh and Andrew Su liked this
The web as a tool - rather than a threat - http://www.slideshare.net/Cameron...
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Eric Logan, Slavomira Vladimirova, Claudia Koltzenburg and 11 other people liked this
Better late then never ;-)
- AJCann
These end up being a bit of a monster so require decent upload bandwidth to get them up there. My poor home connection is struggling somewhat.
- Cameron Neylon
So you're claiming it took 5 days to upload them? :-) Did you see the video? http://bit.ly/3J0vyS Shame you didn't go "Beep" when you changed the slide so people could follow along ;-)
- AJCann
@ajcann Richard has a very annoying doorbell noise he adds to his slide transition, keeps the students awake and then he uploads with mp3 audio recording of the presentation, so you can join the two together. I think he's the only person still using our mp3 recorders from the techdis project!
- Jo Badge
Nope. I'm claiming I didn't have a decent internet connection till yesterday and thought I deserved at least one day of rest :-) Hmmm, wonder if you could set up a high pitched sound off the computer that would be picked up by the camera but not audible? I might try and pull the audio off the video and see if I can do a slidecast at some point. I haven't watched much of the video though - can't stand watching myself...
- Cameron Neylon
I usually do a shortened mp3 for my talks which I sync up on Slideshare before the talk. I suspect people are less tolerant of me droning on online than during a talk. I know I am. As Guy Kawasaki says of PowerPoint presentations with too much text, I can think faster than this bozo can talk.
- AJCann
That's true - hence I try to put enough text on the slides to make them more or less self sufficient. Doesn't always work of course. Especially if there is a big chunk of live demo missing...
- Cameron Neylon
And video of this talk is available at: http://redux.nexgenta.com/people...
- Cameron Neylon
I actually like the single loop in the video, falls well into place in a way :-)
- Claudia Koltzenburg
If we're to get continued funding, and support JBrowse to meet all the
requests that you have justifiably demanded, it's absolutely critical
that we demonstrate an overwhelming demand for JBrowse from the user
community -- that means you. http://sourceforge.net/mailarc...
Khader Shameer, Richard Badge, OpenSci Info and 2 other people liked this
"Also, in another subproject of the same grant, we plan to develop a JBrowse version of the GBrowse_syn synteny viewer developed by Sheldon McKay, so you can browse syntenic regions of homologous genomes side-by-side." definitely convinced me that a letter is in order.
- Paul J. Davis
Thanks for posting!
- Mitch Skinner
About twitter: Trying to get to grips with FriendFeed - http://tw-abouttwitter.blogspot.com/2009...
Mike Chelen, 'Mummi' Thorisson, Jo Badge and 2 other people liked this
Cameron Neylon -- not as annoying as Scoble, but a great Friendfeed evangelist nevertheless
- Benjamin Tseng
Jo's original post is here: http://tinyurl.com/ykq2yj3 Mine's coming on Monday.
- AJCann
What are you using to visualize biological networks? - http://www.flickr.com/photos...
Sutee Dee, Khader Shameer, Piotr Byzia and 10 other people liked this
[Image: "network" by Simon Cockell, link to original source for attribution] In particular, what are you using to view networks in a dynamic way? Cytoscape seems the behemoth for visualizing biological networks, but have you used other solutions? A group mate and I have been discussing how we could *really* use a JavaScript library that rendered as SVG in a web browser. This would allow us to call for more data from our databases and present data on the fly and only-as-needed. He's convinced we could start writing one; I'm concerned it's a lot more difficult than he thinks, but we're both fishing for other ideas.
- Chris Lasher
from Bookmarklet
for working with SVG and Javascript, maybe try svgweb http://code.google.com/p... or Raphaël http://raphaeljs.com/
- Mike Chelen
We're using Raphael in the Protein Geometry Database <http://pgd.science.oregonstate.edu/> for rendering our graphs. It's been a huge boon to cross-browser compatibility since IE *still* can't do SVG.
- Donnie Berkholz
You might try a particle demo on Chromium's canvas element. Other than that I think the optimizations for performance could end up being the bigger project. Not undoable, just maybe not worth the time. Also, specifically Chromium as they're canvas element is current the best, though hopefully FF and Safari aren't too far behind. For IE, just give them a link to Chrome Frame ;)
- Paul J. Davis
Is this meant for big graphs? Is the focus on layouts etc? Prefuse is a pretty nice toolkit for graph layout/calculations. igraph also is an excellent library with a bunch of layout algos
- Rajarshi Guha
Many thanks for your input, guys. @Rajarshi We have graphs of 5k-12k nodes and 20k-80k edges. I don't know if that counts as large but they're not small. @Paul I'm worried about performance (responsiveness) given that Firefox can take a pounding in some of the demos at http://www.chromeexperiments.com. That's why I wonder if Cytoscape is really the only option (right now). @Mike and...
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- Chris Lasher
Thanks, Chris! I certainly hope it enables some folks to do interesting science instead of just looking pretty, though. =)
- Donnie Berkholz
Seventh graders describe scientists before and after a visit to Fermilab. - http://ed.fnal.gov/project...
Euan, Steve Koch, Matthew Todd and 16 other people liked this
This one is lovely: "Their jobs sound very interesting because they can do whatever they want and they still get paid for it." ;-))
- Yaroslav Nikolaev
Drawings of Scientists - http://ed.fnal.gov/project...
Björn Brembs, Pedro Beltrao, Steve Koch and 4 other people liked this
[Found via Pedro Beltrão] "Seventh graders describe scientists before and after a visit to Fermilab."
- Chris Lasher
This is freakin awesome
- Shirley Wu
from twhirl
my favorite one: http://ed.fnal.gov/project... "Hello, I am a regular person!"
- Marie is organized.
I noticed a couple drawn by girls changed genders - from male to female.
- Andrew Lang
Neil Saunders, Brian Krueger - LabSpaces, John Dupuis and 9 other people liked this
Awwwwwwwww.
- Bill Hooker
Congratulations Dr father Gunn
- Nils Reinton
Congratulations!
- Chris Lasher
Congratulations!
- Yann Abraham
Congrats William!
- Walter Jessen
So cute!
- Stephen Francoeur
My contribution to Wikipedia - http://plindenbaum.blogspot.com/2009...
Steve Koch, Andrew Su, Yann Abraham and 3 other people liked this
I spotted several duplicates and talk pages too...
- Egon Willighagen
Yes, that's why I said my 'count' was lower than those ~165 entries. :-)
- Pierre Lindenbaum
How did you compile the list? Wondering what my count is... not created so much as you, and still am impressed by your productivity... even if 165 is the upper limit :)
- Egon Willighagen
@Egon I used the wikipedia API to get my contributions: http://en.wikipedia.org/w... . Creating an article is actually fast thanks to my friefox/WP extension: http://tinyurl.com/9druf2 and a xslt stylesheet pubmed2wiki: http://code.google.com/p... . Biographies are found using this pubmed query http://tinyurl.com/ygsuz38
- Pierre Lindenbaum
Pierre's secrets revealed!
- Andrew Su
Not so bad: I've created 153 new articles in en.wikipedia.org. Most articles are biographies of scientists.
Piotr Byzia, Alberte Denis, Ola and 12 other people liked this
Let me take the opportunity to say: thank you!
- Laurent
What Laurent said. Bravo!
- Bill Hooker
Damn you wikipedia, so addictive! Well done Pierre, very impressive.
- Dave Lunt
very impressed about the number of new articles on #wikipedia by Pierre too!
- Egon Willighagen
Thank you, Pierre!
- directeur
@Pierre so which ones are they? :-)
- Duncan Hull
@Duncan: here they are :-) http://plindenbaum.blogspot.com/2009...
- Pierre Lindenbaum
@Pierre you've been busy!
- Duncan Hull
Plotzie, My Google Wave Robot - http://lee-phillips.org/wave...
Chris Miller, Claudia Koltzenburg, Peter Miller and 4 other people liked this
A google wave robot that takes lists of numbers and converts them to sparklines. Interesting because it does image insertion and other things but also because of the sparkline webservice it uses and the way it gets around appengine limitations
- Cameron Neylon
Good stuff. After looking at Cameron's ChemSpidey, Igor, and now this, I'm really getting excited about the potential for bots and in-line modification of the info-stream.
- Todd Harris
The (im)permanance of online biological resources - http://toddharris.net/blog...
Andrew Su, Tom.Pasley and Pierre Lindenbaum liked this
This has always been an issue, outside of any specific discipline... it would be good to have someone host a virtual image which was a production snapshot for interested parties to download, and run as needed.
- Tom.Pasley
Personally, I think not every app should be actively maintained. Some tools (many/most?) deserve to gracefully fall away into obscurity if they aren't being used. it just doesn't make sense to maintain them, and it increases the cruft that end users have to sort through to find the best tools. OTOH, if you're getting _lots_ of requests and feedback, then I think that would be motivation to find continued funding. Having said all that, the VM idea is a pretty good one...
- Andrew Su
Andrew - Good point. Sustained demand for a resource makes a good case for at least maintenance levels of funding. And I agree - there is a huge amount of noise with circulation of old tools and info (like Googling a problem and getting results from 2007 - always suspect). Still, so many bioinformatics projects generate resources and not always publications. It seems like we need a place to archive this content.
- Todd Harris
@Tom You're right. And I'm certain that other fields have already made in-roads in this area. Would be good to leverage that experience.
- Todd Harris
RT @CameronNeylon: I wonder if the early days of email was like this. People ringing up to ask what your email address was? #googlewave
John Hogenesch and Andrew Su liked this
Linux is an Evil and Uncompassionate OS - http://www.geeksaresexy.net/2009...
Andrew Su liked this
MYAHAHAHA!
- Paul Gardner
MYAHAHAHA!
- Paul Gardner
The Protein Box Bot code for autoupdates of the Gene Wiki can be found at: http://code.google.com/p...
Nakao M., Mike Chelen, Andrew Su and 2 other people liked this
I love the "PBB" stuff we posted at Google Code, but it's admittedly a bit stale (in the services that it consumes and in the format it outputs). The new tool we have is at http://biogps.gnf.org/GeneWik... (for example, for PRKACB: http://bit.ly/332ed3). Right now this tool is only used for manual updates/additions, but it exports XML so we're planning on wrapping it in a script for mass updates as well...
- Andrew Su
Andrew, is the BioGPS code available? I was looking into PBB to extend what you've done but for genes from model organisms. There is a wealth of highly curated information I want to seed (and have the bot maintain).
- Todd Harris
Todd, don't know how I let this one slip by, sorry for the delayed response. You're interested in BioGPS code or PBB code? Both are possible, but both have challenges. Would love to think about working together if you've got something in mind...
- Andrew Su
ahh, now I get it, our BioGPS plugin for creating Gene Wiki content. yup, definitely possible. But you should know that due to WP's infamous "notability" guideline it can be hard to get model organism info put in en masse, but it's worth giving it a shot...
- Andrew Su
Sage Bionetworks Update: building an OA standard for human disease biology http://pimm.wordpress.com/2009... http://sagebase.org/
Greg Tyrelle, Mr. Gunn, OpenSci Info and Andrew Su liked this
I am looking for a simple option to retrieve the mesh terms and publication date for a given PubMed ID. I was looking at Eutils tools like esearch and efetch. But not able to find the exact details or URL format to query PubMed using key workd and print only publication date and mesh fields - any suggestions ?
Paul Bacchus, Mike Chelen, Abhishek Tiwari and 2 other people liked this
If you're looking for a given ID, try this -- http://eutils.ncbi.nlm.nih.gov/entrez... -- then use grep to extract all lines which start with MH to get the MeSH keywords
- Andrew Clegg
Obviously you need something like curl or wget which can run from a script and download from a URL. If you need to search by something other than PMID (e.g. a text query), use esearch to run the query and get back the IDs, then efetch to download the docs corresponding with those IDs. Does that make sense?
- Andrew Clegg
e.g. to get all MeSH terms and the pub date for PMID 19614587, try this (from a Mac or Linux command line anyway): curl -s 'http://eutils.ncbi.nlm.nih.gov/entrez... '^(MH |DP )' -- ARGH, FriendFeed being 'helpful' has mangled the command and I don't know how to override that. If you give me an email I can send better instructions :-)
- Andrew Clegg
Download you data as XML ( http://eutils.ncbi.nlm.nih.gov/entrez... ) and then extract the MESH terms using XSLT. Do you need help for this ? For example, see the http://code.google.com/p... in my repository.
- Pierre Lindenbaum
Pierre, mere mortals can't write XSLT. ;) At least I failed miserable the last time I tried to do something simple
- Michael Kuhn
tutututu, XSLT is simple for simple things (http://www.w3schools.com/xsl... ) . and XSLT is complicated for difficult things ( http://docbook.sourceforge.net/release... ). I mean , it takes less than one hour to make a simple task with XSLT.
- Pierre Lindenbaum
and the more people wil use XML+XSLT or RDF, and the more you will work with structured data instead of parsing/grepping/sorting meaningless tab-delimited files.
- Pierre Lindenbaum
Yes, it's only starts to become fun when you are pulling XML from more than one document :)
- Egon Willighagen
personally, I would use an xpath library to parse the xml and output in plain text. my understanding is that xslt (which uses xpath) is great for parsing xml but pretty much is designed to output XML or HTML only.
- Andrew Su
@andrew : can you use Xpath without programming ? which of tool is it ? Anybody can use XSLT as most browser embed an internal XSLT engine. You just have to add the URL of your stylesheet at the top of your XML document ( http://www.w3schools.com/xsl... )
- Pierre Lindenbaum
Seriously guys -- XPath/XSLT is overkill for this kind of thing. It's a one-liner. I've written is up here so it doesn't get mangled this time: http://biotext.org.uk/how-to-...
- Andrew Clegg
working code wins! ;) (But I will say that learning to use the perl XPATH library was surprisingly simple, even for someone whose skills are decaying as fast as mine...)
- Andrew Su
@Andrew C.. yes of course , I agree :-)
- Pierre Lindenbaum
BTW XMLStarlet is great for doing XPath/XSLT/etc. from the command line -- http://xmlstar.sourceforge.net/ or you may already have it as /usr/bin/xml -- but try it the easy way first ;-)
- Andrew Clegg
Andrew C, where I think your one-liner gets a bit more complicated is when you request multiple documents (e.g., http://eutils.ncbi.nlm.nih.gov/entrez...) and then want to parse out multiple fields from each article on a single line. That I think is where the balance shifts a bit toward xpath...
- Andrew Su
@Andrew Yeah, it very much depends on what you want to do *next*...
- Andrew Clegg
from email
recently, @tpoi asked for a tool returning the number of paper per year ( http://twitter.com/tpoi... ). I wrote this stylesheet http://code.google.com/p... . He was then able to compute the result without knowing any command-line tool, but using his browser.
- Pierre Lindenbaum
(sorry to everyone else for hijacking this thread, but...) Pierre, very cool. How do you invoke your xsl? you need to reference it in an XML doc, right?
- Andrew Su
1) you can invoke a XSLT engine e.g. http://xmlsoft.org/XSLT... "xsltproc style.xsl doc.xml" 2) you can add a stylesheet url at the top of your XML document and open this document in firefox . See "Link the XSL Style Sheet to the XML Document" in http://www.w3schools.com/xsl...
- Pierre Lindenbaum
@All : Thanks a lot for the awesome responses. Let me go through them and try them. I was working on to contribute to GeneWiki3 (Thanks to Andrew Su, he assigned a small module for me to contribute to GeneWiki3) This is a true Science 2.0 learning experience. Thank you all !!
- Khader Shameer
More fun with links -- from Lifehacker "Top 10 Web Collaboration Tools that are not Google Wave" http://lifehacker.com/5373339...
Daniel Mietchen, Joel Zehring and Andrew Su liked this
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