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Rajarshi Guha › Likes
Bioteam and cloud computing http://www.bio-itworld.com/issues... #aws
Anna Croft, Justin H. Johnson and Rajarshi Guha liked this
Mel Reichman on Pool Shark’s Cues for More Efficient Drug Discovery - http://usefulchem.blogspot.com/2009...
Rajarshi Guha liked this
I cannot begin to describe how absolutely PERFECT this is. - http://www.reddit.com/r...
Noel O'Boyle, Marcos de Carvalho, Rajarshi Guha and Pierre Lindenbaum liked this
Review Of The Fingerprints Of God - http://www.scientificblogging.com/chemist...
Rajarshi Guha liked this
I found the premise of Barbara Bradley Hagerty's new book "Fingerprints of God" quite intriguing. The author, raised as a Christian Scientist, attempts to look into alternative religions and science to see if her faith is justified. There is nothing really new here - in terms of topics that have been covered in many other popular books. But what I found interesting was her interpretation of her experiences and investigations. She chronicles her struggles and revelations in an autobiographical format - and I'm usually a sucker for autobiographies. read more
- Jean-Claude Bradley
40 Seriously Funny Print Ads - http://www.webdesignerdepot.com/2009...
Rajarshi Guha liked this
I love the cassette/ipod one
- Rajarshi Guha
Visualization code and resources - http://chapmanb.posterous.com/visuali...
Rajarshi Guha liked this
There have been a number of great posts recently with visualization tips: - Rajarshi describes customizing R heatmaps, which are immensely useful for things like visualizing next-generation sequencing results across tiles: http://blog.rguha.net/?p=419 - Revolution computing reviews R code for ti ...
- Brad Chapman
from Posterous
the time series visualization is pretty cool
- Rajarshi Guha
Andrew Lang, Rajarshi Guha, Andrew Perry and Mary Canady liked this
"A pizza whose diameter equals z and thickness equal a, will have a total volume of V= pi*z*z*a" -- @Moataz_mokhtar (via @embee)
Derrick, ashish, Rajarshi Guha and Mike Chelen liked this
I hope I am not wrong, I think the radius -not diameter- should be "Z".
- ashish
I seem to remember that you are right about the radius actually.
- Thomas Bøhm
Building a simple Expression language with JJTree/Javacc . My Notebook - http://plindenbaum.blogspot.com/2009...
Rajarshi Guha liked this
CCL: Sheffield Chemoinformatics Conference 2010: Call for Papers - http://ccl.net/cgi-bin...
Rajarshi Guha liked this
Webel - a web service based python library for chemical information - http://baoilleach.blogspot.com/2009...
Deepak Singh, Rajarshi Guha and Peter Miller liked this
Potentially a nice simple library for implementing in AppEngine based web services and/or Wave robots. Simple text search, MW, SMILES etc. Or I could finish wrapping the ChemSpider API properly...
- Cameron Neylon
Call for Collaboration: JavaDoc validation with OpenJavaDocCheck - http://chem-bla-ics.blogspot.com/2009...
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Rajarshi Guha liked this
Nov 10, 2009: Cambridge Clojure Interest Group Meetup at The Kingston Arms - http://upcoming.yahoo.com/event...
Egon Willighagen, Deepak Singh and Rajarshi Guha liked this
Organised by the very functional coding trombonist Jim Downing http://jimdowning.wordpress.com/2009...
- Duncan Hull
Na... Na... Na... I am not listening.... Na... Na...
- Egon Willighagen
@Egon resistance is futile :-)
- Duncan Hull
Artemether: Entity of the Month « O'Really? - http://duncan.hull.name/2009...
Rajarshi Guha and Egon Willighagen liked this
November’s entity of the month at ChEBI is the antimalarial drug Artemether. This accompanies release 62 of ChEBI, not just yet another incremental release but an increase of more than twentyfold in the number of entities in ChEBI, thanks to merging of data between an updated ChEBI [1] and ChEMBL [2]. ChEBI now (as of release 62) has over 455,000 total entities, compared to over 18,000 in the previous version (release 61), see ChEBI news for details. The text below on Artemether is reproduced from the ChEBI website:
- Duncan Hull
from Bookmarklet
More importantly... it has JChemPaint as OpenSource structure drawing editor
- Egon Willighagen
@Egon absolutely http://egonw.posterous.com/congrat...
- Duncan Hull
I am very pleased that our new design is really paying off... the current applet would not have been possible with the old code base...
- Egon Willighagen
Does this mean rendering code will be merged soon into cdk master?
- Rajarshi Guha
@Rajarshi you'll have to ask Stefan, Mark or Egon: I'm not an expert on JChemPaint...
- Duncan Hull
Rajarshi, we are working hard on this... but the code is far from CDK stable... see the reports here: http://pele.farmbio.uu.se/nightly... look for the render* and control* modules... Then, there is the other thing that the current EBI applet is not based on the latest JChemPaint primary code, and we are scheduling a meeting to make that happen too... it's a lot of code, complex code, but we are getting there...
- Egon Willighagen
That said, the above linked nightly does allow you to download a working rendering and editing library already, based on CDK master (of a few weeks ago, see the git history)...
- Egon Willighagen
Introducing Webel - A cheminformatics toolkit built solely on webservices - http://baoilleach.blogspot.com/2009...
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Cameron Neylon, Yann Abraham and Rajarshi Guha liked this
Nice!
- Yann Abraham
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
Must not optimize Python scripts that already just take 1 sec (and which I'll run only 10 times). Must not optimize Python scripts that ...
Pedro Beltrao, Deepak Singh, Rajarshi Guha and Jesse Newhart liked this
Congratulations to Mark, Stefan and Christoph for bringing JChemPaint to ChEBI! - http://egonw.posterous.com/congrat...
Jean-Claude Bradley, Frank, Duncan Hull and 2 other people liked this
Posted via email from Egon's posterous
- Egon Willighagen
from Posterous
Gapminder: Dramatic changes in girls’ age at first marriage http://www.gapminder.org/world-b...
Chris Miller, Steve Koch, Neil Saunders and 2 other people liked this
amazing stuff - it would have been nice to have a submission for our chemviz symposium at the ACS of some type of chemical application
- Jean-Claude Bradley
Atheist Sees Image of Big Bang in Piece of Toast: http://www.satireandcomment.com/0208toa...
Mr. Gunn, Chad Orzel, Pedro Beltrao and 4 other people liked this
LOL!
- Christian (Simply X)
Milestones... - http://chem-bla-ics.blogspot.com/2009...
Steve Koch, Björn Brembs, Jean-Claude Bradley and 3 other people liked this
Impressive Egon.
- Andrew Lang
New Bioclipse Features: Kabsch Alignment, RMSD Distance and Tanimoto Simarlity Matrices - http://chem-bla-ics.blogspot.com/2009...
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Rajarshi Guha liked this
Initiative targets malaria eradication - http://www.nature.com/news...
Rajarshi Guha and joergkurtwegner liked this
Fast building SMILES structure viewer with Dingo and WPF - http://blog.charliezhu.com/2009...
Rajarshi Guha liked this
Welcome to Hama project - http://incubator.apache.org/hama...
Rajarshi Guha liked this
Hama (means a hippopotamus in Korean) is a distributed scientific package on Hadoop for massive matrix and graph data. It is currently in incubation with Apache. The main goal of Hama is to provide computational tools for data-intensive scientific and industrial areas. It consists of two packages, which are the matrix package and the graph package.
- Deepak Singh
Gathering Physicochemical Data Onto ChemSpider - http://www.chemspider.com/blog...
Abhishek Tiwari, Rajarshi Guha, Egon Willighagen and 3 other people liked this
"they derived a simple equation based on the number of carbon atoms, NC, and the number of hetero atoms, NHET: log P = 1.46(±0.02) + 0.11(±0.001) NC – 0.11(±0.001) NHET" - since we are using the calculated LogP as a descriptor for solubility predictions, wouldn't the use of NC and NHET be mathematically equivalent if this relationship is good?
- Jean-Claude Bradley
Yes, that's exactly what their equation is saying. I gave one example on the blog post for toluene compared to the multiple other predictions and, more importantly, the single experimental data point. I have 2 other data points that are comparable. This single data point suggests that their simple equation gives better values than the CDK but we should check it against the other points...
more...
- Antony Williams
The gathering of LogP data is coming together pretty well..I've got over 4000 unique structures with experimental logP values and still looking for more. Eventually it will all end up on ChemSpider
- Antony Williams
That's great Tony - that means we might be able to get even better predictions looking at specific classes of compounds
- Jean-Claude Bradley
Tony, quick question (not really related): are there any educational materials available (yet) for Chemspider - I've just discovered a teaching hole I need to fill next week and figured that I want to introduce the kids to Chemspider, possibly coupled with running their own (simple) computational calculations to compare the data ...
- Anna Croft
Anna I've used ChemSpider for various educational assignments - see the one I added yesterday under "puzzles" http://getcheminfo.wikispaces.com/assignm... I have also asked students to explain NMR spectra: http://chem242.wikispaces.com/extracr...
- Jean-Claude Bradley
Antony... seconded: please file a feature request at http://cdk.sf.net/
- Egon Willighagen
Jean-Claude... what's the DOI for the paper behind that equation...
- Egon Willighagen
Egon - from Tony's post the link to the paper is http://www.vcclab.org/article...
- Jean-Claude Bradley
@Jean-Claude looks a bit too advanced for our lot, but I'll read through in more depth when I'm back from my next class
- Anna Croft
Egon..I'm sorry...what were you seconding for me to add as a feature request?
- Antony Williams
That simple LogP equation...
- Egon Willighagen
I am implementing it now...
- Egon Willighagen
BTW, the quality of LogP algorithms can be easily judged if you consider that this simple equation does very competitive but does not distinguish between ethanol and methoxymethane.
- Egon Willighagen
Implemented at: http://github.com/egonw... against CDK 1.3.x (but needs review first)
- Egon Willighagen
Patch approved and applied to CDK 1.3.x... jar should be downloadable tomorrow from http://pele.farmbio.uu.se/nightly...
- Egon Willighagen
Egon...re. your comment about methoxymethane vs ethanol...the difference is 0.1 vs -0.3. How does the CDK do with this?
- Antony Williams
nC=2, nHET=1 -> 1.46 + 0.22 - 0.11 = 1.57.... so, I'd say the difference between CCO and COC is indeed well within the method prediction error :)
- Egon Willighagen
Yup...I'd say that is a failure :-)
- Antony Williams
Yes, it also says very much about all those more complex methods :)
- Egon Willighagen
Maintaining patches is fixing patches - http://chem-bla-ics.blogspot.com/2009...
Rajarshi Guha and Mike Chelen liked this
We are the Robots. A first attempt at a proteomics robot for Google Wave. http://neilswainston.blogspot.com/2009...
Mackenzie Cowell, FedericaB., Joseph Jose and 12 other people liked this
Replied on the blog but will try to give this a go ASAP...but probably not today...
- Cameron Neylon
Hi Cameron. Can't make your Hackfest, I'm afraid, although I'd love to attend virtually if possible...
- Neil Swainston
Cool - will keep you in the loop as to the mechanics of that. Need to find fifteen minutes to think the best approach through.
- Cameron Neylon
hey neil, looks good
- Duncan Hull
Cheers, Duncan. Are you one of the cool kids with a Wave account? If so, does it work?!?
- Neil Swainston
Hi all those who liked. Did anyone try it in a Wave? Does it work? Thanks in advance for any help / feedback.
- Neil Swainston
Arrggh. Sorry, yes we tried and it seems to be broken. This probably just requires a few cycles of deploy and test but I'm not really in a position to do that this week. Maybe next week?
- Cameron Neylon
Thanks, Cameron. I'll keep prodding semi-interested parties. Can I also please reiterate my plea for an invite if any are lying around - the deploy and test cycles should be reduced if I can do the testing myself! Thanks.
- Neil Swainston
Neil, I have invites. If you have a GMail address, DM it to me, or else I'll use your Manchester one.
- Neil Saunders
Did we get Neil Swainston in in the end?
- Cameron Neylon
Neil Saunders has put me down for one. Just waiting for Mr Google to put it in the envelope and post it.
- Neil Swainston
Cool, good to know. We'll see you on the inside then
- Cameron Neylon
from twhirl
*pokes google*
- OpenSci Info
from IM
Thanks to Neil. I've got my account, and - would you believe it - the robot was kaputt. Amongst other things, Waves and Applets are not immediately happy bed-fellows... As I expected, I guess. Hmm...
- Neil Swainston
Neil, we can probably make some time to do some trouble shooting and testing in Wave this week perhaps? There are lots of little gotchas that are reasonably easily fixed.
- Cameron Neylon
Thanks Cameron. That would be very much appreciated. I made a fair bit of progress yesterday - it's a case of sticking applets within Gadgets. It now pretty much works. However, the applets periodically, and mysteriously, disappear. Any debugging tips from anyone?!?
- Neil Swainston
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