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
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
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
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
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
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
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
"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
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
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
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
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