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Andrew Lang › Comments
Google now indexing thumbs. Final page of solubility book: Solubilities of inorganic and organic compounds: a compilation of ..., Volume 1 By Atherton Seidell
Stephen Francoeur, Steve Koch, Jean-Claude Bradley and 2 other people liked this
it actually looks like a toe
- Jean-Claude Bradley
Correct. Tis pink, looks like a form of shoewear with desert like background to me so, might this be "Toe in the Sahara, with shoe" Featuring Sting and @cromercrox :- http://www.last.fm/music...
- Graham Steel
or does this prove Megan Fox made this scan http://www.nydailynews.com/gossip...
- Jean-Claude Bradley
That's this one, right? http://www.archive.org/details...
- Egon Willighagen
Is this already be digitized by typing monkeys?
- Egon Willighagen
it is automatically generated Egon - just waiting for me to get the preface done....
- Jean-Claude Bradley
Jean-Claude... you mean, you are getting the data rescued already?
- Egon Willighagen
no sure what you mean by rescued Egon
- Jean-Claude Bradley
@JC I think Egon is talking about people transcribing the Seidell's solubility book. @Egon I think JC is talking about the ONS solubility book. :)
- Andrew Lang
thanks for the clarification Andy - Marshall already uploaded most of the carboxylic acids and aldehydes - yes I was referring to our own book Egon
- Jean-Claude Bradley
Ah... JC, sorry... I did not realized you were compiling an own book :) @Andrew... yes, I was talking about transcribing values from the Seidell book... I might know someone who wants to help with that (or at least try it; he's not a chemist)...
- Egon Willighagen
My mistake Egon about the confusion with the book - yes we have one coming out soon. As for help with adding data from the Seidell book I think we have most of the relevant compounds. And it would require a chemist to translate the way names were done back then - also much of it requires conversion between g/100g solvent or g/100g solution to molar, etc
- Jean-Claude Bradley
Unemployment Visualization http://www.nytimes.com/interac...
3.9% for white male college graduates ages 25-44.
- Andrew Lang
48.5% for black males without high school diplomas ages 15-24.
- Andrew Lang
log P = 1.46(±0.02) + 0.11(±0.001) NC-0.11(±0.001) NHET
Jean-Claude Bradley liked this
Is it really that easy? http://www3.interscience.wiley.com/journal...
- Andrew Lang
Just noticed - this is from vcc lab.
- Andrew Lang
like a dream come true
- Jean-Claude Bradley
@Andrew... no, it's not that easy... it's that *difficult*... the problem is so complex, it's very hard to do better...
- Egon Willighagen
Ubiquitous information technology fields - http://futurememes.blogspot.com/2009...
Jean-Claude Bradley liked this
"...once any area becomes an information technology, it starts conforming to the exponential curves of Moore’s Law..."
- Andrew Lang
great post - if we can figure out a way to automate the execution of the DoSol sheet it should go exponential - that is our bottleneck right now
- Jean-Claude Bradley
Invisibility Uncloaked - http://www.sciencenews.org/view...
Didn't know about this part of the story "But it was another PRL reviewer’s rebuke that opened Leonhardt’s eyes wide. It said he was not alone. The assessment, routinely shared with Leonhardt, indicated that the reviewer had been to two meetings in the previous months “in which John Pendry discussed his group’s efforts on the same issue, calling it a cloaking device or their Hogwarts project in reference to the cloak of invisibility associated with the Harry Potter series.” Pendry and his colleagues, the assessment added, “supposedly have filed a patent related to this work.” Hence, the anonymous reviewer declared, the work was not new and did not merit publication in PRL."
- Andrew Lang
Abstruse Goose: Rite of Passage - http://abstrusegoose.com/
Björn Brembs, Richard Akerman, Pierre Lindenbaum and Andrew Lang liked this
#qotd Computer Science Major "WTF, Man. I just wanted to learn how to program video games"
- Duncan Hull
from Bookmarklet
Too true of computer science majors these days.
- Andrew Lang
I like abstractions
- Richard Akerman
from BuddyFeed
OMG this is the best paper in years - http://isotropic.org/papers... - HT to Jessica Green for pointing this out
Dan Gezelter, Bosco Ho, Mickey Kosloff and 6 other people liked this
...and here's the presentation of the paper: http://www.youtube.com/watch...
- Michael Kuhn
it is excellent. I'm not so sure about that part about chicken though.
- Richard Akerman
What a great find!
- Chris Lasher
Certainly seems to refute earlier work by C. Sanders.
- Matthew Todd
Chicken. Chicken chicken chicken.
- Bosco Ho
Rhubarb Rhubarb - http://en.wikipedia.org/wiki...
- Andrew Lang
http://itre.cis.upenn.edu/%7Emyl... This gives links to fill in the back story.
- Chris Lasher
Chemistry in Second Life republished on PubMed - http://www.ncbi.nlm.nih.gov/pmc...
Elizabeth Brown, Peter Miller, Antony Williams and Andrew Lang liked this
Article on Chemistry in Second Life by Lang and Bradley published in Chemistry Central Journal automatically republished in PubMed. Gotta love Open Access.
- Jean-Claude Bradley
The did a good job of porting it over too.
- Andrew Lang
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
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
Webcite can be used to archive an Excel version of the Solubility Summary spreadsheet - here is the Nov 3, 2009 archive: http://www.webcitation.org/5l12V0P... All formulas and web services called are retained - they would not be in other formats such as CSV. This will work with any Google Spreadsheet - convenient for formally citing a database
Marcin Wojnarski, Steve Koch, Daniel Mietchen and 6 other people liked this
Now that's good to know!
- Cameron Neylon
That's brilliant.
- Andrew Lang
I just uploaded another version - notice how it gives you a dropdown for the cached version on the top right. You can now create a hyperlink to a specific cached version like this http://www.webcitation.org/query...
- Jean-Claude Bradley
Brilliant stuff. I'm becoming a big fan of WebCite - will use the service for the bulk of the Web refs in my thesis. The versioning functionality may come in handy.
- 'Mummi' Thorisson
Mummi - I had experimented with it a long time ago and there were some issues that led me to drop it. There are still issues - for example when they alert you to the fact that your submission is archived they don't give you all the citation information - have to remember to copy and paste all that info given on the website itself right after submission. I also don't know what happens to...
more...
- Jean-Claude Bradley
Chemistry in Second Life paper in Chemistry Central Journal - http://usefulchem.blogspot.com/2009...
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ffcode, Mike Chelen, OpenSci Info and 5 other people liked this
My Xstreet account has seen a very sharp uptake on the number of people getting our stuff. I have had to log in to SL just to make sure my messages are not capped. I'm sure it will die down soon but pretty cool to see.
- Andrew Lang
where is the best place to find source code for these items, is http://opensledware.wikispaces.com/ still active? great article, congrats!
- Mike Chelen
Last time I checked the wiki was mainly taking spam. I think Desideria Stockton runs it and she's not been inworld a lot lately afaik
- Peter Miller
The final format just got published http://journal.chemistrycentral.com/content... which is nice because you don't have to download the pdf for the full text version
- Jean-Claude Bradley
Chemistry in Second Life - http://www.journal.chemistryce...
Mike Chelen, Berci Mesko, MD, Peter Miller and 3 other people liked this
Sheesh, 23MB PDF !
- Rajarshi Guha
It's all the pretty pictures.
- Andrew Lang
no substitute for images to describe Second Life projects
- Jean-Claude Bradley
Would be nice if one could transform a scene into something 3D portable... and I'd be happy if that would extend 100m or so, with the far scenery as images on the 100 circular wall around the scene... (tune 100m where you like)
- Egon Willighagen
could you use Jmol Egon to depict 3D scenes?
- Jean-Claude Bradley
Well, at least the molecular bits...
- Egon Willighagen
Not sure what is meant by "3D portable". SL certainly has its limitations though the Meerkat viewer and its ilk can be used to archive structures offline though I haven't tried it with any molecules yet. In principle the molecules can also be uploaded to OpenSim grids which can run standalone and, I believe, in a web browser too. You could use the VR room or a holodeck/holoemitter to provide a context. Great paper btw.
- Peter Miller
Ah, I should have said that using Meerkat works fine with the protein sculpted prims, at least as far as SL is concerned. Just tried it with one of the molecules generated using Andy's older molecule rezzer and that works fine too: 145 prims rezzed and linked in about a minute.
- Peter Miller
And just confirmed that you can upload said molecule in an OpenSim grid (Intel's ScienceSim to be precise).Not sure whether Andy has already done this, nor indeed whether any of his rezzers work in OpenSim. I suspect the molecule rezzed in the same sim position it was archived in -- which could be inconvenient though Meerkat shows your own content in the mini-map clearly enough.
- Peter Miller
@Peter. Great stuff - I've never tried OpenSim - didn't know you could transfer content. Cool.
- Andrew Lang
Short blog: http://tidalblog.blogspot.com/2009...
- Peter Miller
Final (pretty) version released, pdf only 5.7 MB :)
- Andrew Lang
Open Chemical Data #1: NMRShiftDB - http://chem-bla-ics.blogspot.com/2009...
Egon Willighagen, Mike Chelen and Andrew Lang liked this
some 'open data' on ChemSpider.
- Andrew Lang
what would be the best way to mirror the data and interface, is nmrshiftdb-data-1_3_4.sql.gz and the applet all that is needed?
- Mike Chelen
Egon would be the person to ask about that
- Jean-Claude Bradley
Mike, I guess it depends on how you like to mirror it... you could talk to Christoph Steinbeck in setting up a node in the NMRShiftDB network... alternatively, you could simply make the data available using a custom (read-only) web interface. I recently starting offering the NMRShiftDB data (GNU FDL license) as RDF triples, now mirrored by, for example, Bio2RDF...
- Egon Willighagen
Egon: hopefully something that can be downloaded and reused or modified, would it help to bundle the SQL and RDF data together with the applet?
- Mike Chelen
I think you can download the whole lot from sf.net/projects/nmrshiftdb, but never installed the full thing myself...
- Egon Willighagen
TwirlyMol - Status update re world domination - http://baoilleach.blogspot.com/2009...
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Peter Miller, Jean-Claude Bradley and Andrew Lang liked this
here's the demo: http://www.redbrick.dcu.ie/~noel...
- Andrew Lang
Flickr as a paintbrush - http://www.cartogrammar.com/blog...
Steve Koch, Jesper Lind and Jean-Claude Bradley liked this
Cool visualization.
- Andrew Lang
let the remixing never end
- Jean-Claude Bradley
Molecules in motion... - http://tidalblog.blogspot.com/2009...
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Jean-Claude Bradley and Andrew Lang liked this
'quantum teleportation' of molecules between grids.
- Andrew Lang
I was surprised how easy it was -- I was expecting problems and there were hardly any.
- Peter Miller
Should we contribute the solubility data to Wolfram Alpha? http://www.wolframalpha.com/partici...
Egon Willighagen, Matthew Todd, Jean-Claude Bradley and 2 other people liked this
rdf?
- Andrew Lang
seems like an obvious thing to do if possible - but is it true that there is no way to provide a source for data?
- Jean-Claude Bradley
I'm uneasy with the whole interface for this reason.
- Matthew Todd
I'm uneasy with the lack of attribution for specific data points and the lack of an interface for "corrections" as opposed to just comments. The data has to scale for this to work and I just don't see how they can do that without an open dataset
- Cameron Neylon
content submission policy - "When you submit a fact, set of facts, dataset, formula, or any other information to be considered for incorporation Wolfram|Apha, you are giving it to Wolfram Alpha LLC ("we"/"us") free and clear, to do with anything and everything we choose. Your submission has to include a transfer/disclaimer of all intellectual property rights because ..."
- Andrew Lang
Andrew - what does that mean? Data flow openly in, but not openly out?
- Matthew Todd
@Matthew: I'd say that's exactly what it means. They'll happily take but won't give back. Hell, I could even live with that -- if there were sources provided for the data, rather than a blanket "Trust Us".
- Bill Hooker
Yes. I don't like it much either - I made my suggestion before I found the submission policy - maybe we shouldn't - just as a matter of principle.
- Andrew Lang
I think there is a balance here between being helpful and trying to persuade them to open up the innards more and working just to see stuff dissappear into the bowels of the system. I would start by being positive and see what the response is really. After all it is open data so they can do with it what they like - question of how much effort we are prepared to put in really
- Cameron Neylon
Cameron++ This is a nice example of why people use copyleft data licenses :) If you truly want your data to be Open (CC0, PD, ...), you would not care if WA would remove source info and make the data proprietary...
- Egon Willighagen
Egon agreed. Which is why I phrased it like I did. But equally an example of community enforcement. WA are free to use the data, I would be happy for them to do so. But I'm not going to put much work into assisting them or working with them unless I can see that data being allowed back out in a useful form. To be fair to them they are allowing export of the "Mathematica Form" of their data objects which is presumably what they are holding in their databanks
- Cameron Neylon
Egon, and to be precise I object to them removing source data and making it proprietary because I think it means the service won't ultimately be as useful as it could be. If it were open and user editable then with a growing user curated data set and what appears to be a pretty good natural language parser and reasoning system we could do great things. Closed it won't be as good so I do object and will say so. I just don't think a license on our data is the right way of enforcing their good behaviour :-)
- Cameron Neylon
Wrote up my thoughts... discussion most welcome: http://chem-bla-ics.blogspot.com/2009...
- Egon Willighagen
Don't mind at all if WA wants to vacuum up all the data it pleases, but as Cameron says it alters the motivation for being part of the experiment. I also can't be bothered with it if the data are not sourced and credited. Question to student = x. Student answers y. Student is asked "How do you know?", student replies "Because WA says so" etc
- Matthew Todd
Matthew, indeed! Google has the advantage that it keeps track of the source... this is what worries me about many chemistry databases too: where is the link to the (primary) source... WA is not that different from other recent efforts... BTW, I did see sources for some questions... e.g. the 42 answer did source to D. Adams...
- Egon Willighagen
:) The one thing nobody needs a source for...
- Matthew Todd
Given the amount of curation that goes on with the ChemSpider database it is totally unrealistic to expect that data are immutable "facts" - very dangerous foundation indeed
- Jean-Claude Bradley
Lets say we put some solubility info in there - what would be and example of a query or task that could be performed by WA?
- Jean-Claude Bradley
@ JC: Right - what are the really interesting questions you could use answers to? How about a prediction of other solvents you could try that might dissolve/precipitate a molecule with known (in)solubility in several given solvents. i.e. an extrapolation. Maybe I'm over-burdening WA with expectations, but I have in mind what Michael Nielsen was previously talking about - *discoveries* that have been made through the semantic web, or linked data. Isn't that what would separate WA from a search engine?
- Matthew Todd
@Egon -- "If you truly want your data to be Open (CC0, PD, ...), you would not care if WA would remove source info" -- not quite. I don't care if they come and get my data and do whatever with it -- as you say, that's why it's Open. What I am balking at is the idea that the community should actively provide them with data, only to see it disappear into a black hole. If they want community input they should be prepared to engage fully with the community.
- Bill Hooker
I'm also unhappy - our own studies show that there is no quality control - they hoover everything and use suspect algorithms to deduce from it. There are sources they have used - like MSDS collections that I did not use because I assumed I would broach copyright. Maybe they have paid, but maybe they have stolen
- peter murray-rust
@Bill: yes, I can relate to that. There is so much to do, and independent from license choice, I too do not want to spend (too much) time on something proprietary black hole.
- Egon Willighagen
I actually chatted with Theodore Gray at Google and offered to help with the quality of data on Wolfram Alpha. They do not seem to deal at all with stereochemistry (See the blogpost: http://tinyurl.com/yk7mkyt). I sent an email and can't get a response to even allow us to help improve the quality. If anybody has an inroad to Wolfram Alpha and can introduce me to someone who is...
more...
- Antony Williams
I emailed Theodore Gray after scifoo and he set me up with some W|A peeps, we're converting our calc labs to W|A, but I don't know any of the data people. Separately, I did get a reply from the data people regarding the solubility data: "Thank you for your suggestion regarding Wolfram|Alpha. We are interested in hearing more about your data, please provide us with source links if possible or attach a sample of your excel file." I replied but didn't hear back.
- Andrew Lang
"Thieme is the first publisher to make primary chemistry data accessible worldwide". Analytical data will be made available online via the Thieme eJournals website using digital object recognition in the form of Digital Object Identifiers (DOI)" http://www.thieme.de/connect.... Good data to add to ChemSPider
Andrew Lang and Jean-Claude Bradley liked this
“The data will be permanently saved and, by assigning them a DOI, made accessible and searchable, as well as citable and linkable,” states Dr. Jan Brase from the TIB Registration Agency." Interesting.
- Andrew Lang
I blogged about this tonight.. http://www.chemspider.com/blog.... Anybody want to help process and deposit I'd appreciate the help!
- Antony Williams
The Fate of the Incompetent Teacher in the YouTube Era - http://openresearch.sebpaquet.net/2009...
Mickey Kosloff, Thomas Brox Røst, Berci Mesko, MD and 3 other people liked this
Never heard of Khan Academy before - looks interesting.
- Andrew Lang
Andrew: they are quite good! videos cover many topics, all with the convenience of youtube
- Mike Chelen
So Bad It's Worse - http://xkcd.com/653/
so where do you put the recent Star Trek movie? I know you had some problems with the physics :)
- Jean-Claude Bradley
Red Matter?! It really disturbed my English prof. colleague when I told him the implications - that everything, TOS, STNG, DS9, all the previous movies, etc now effectively took place in a parallel universe.
- Andrew Lang
aren't the previous shows in an alternate (now extinguished) timeline, not a parallel universe?
- Richard Akerman
from BuddyFeed
You're right Richard. They're not going to 'fix' things like they did in the City on the Edge of Forever, for example, that is what disturbed my colleague - he has invested a lot of time in Star Trek. :) "The first one did what it was required to do, which was bring the family together and reset," Abrams explained in an interview with MTV News.
- Andrew Lang
the pace of a planet being consumed by a black hole was amazingly (and dramatically!) gradual
- Mike Chelen
yes, but it was overall much better than the Star Wars Holiday Special. I'm glad they didn't broadcast it in the UK or my life may have gone in a different direction.
- Andrew Lang
Data visualization in Second Life - http://www.flickr.com/photos...
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Peter Miller, Mike Chelen and Jean-Claude Bradley liked this
is the latest version available through xstreet or only drexel island?
- Mike Chelen
'Hiro's molecule rezzer' is stable and is on xstreet. Orac is perpetual beta and is available from Hiro (er... me).
- Andrew Lang
Jesper Lind and Jean-Claude Bradley liked this
javascript based visualization
- Andrew Lang
as you mentioned Andy - similar javascript approach to TwirlyMol from Noel http://ff.im/9tulY
- Jean-Claude Bradley
Interactive 3D Visualisations of Biological Molecules Integrated into the Scholarly Literature - http://usefulchem.blogspot.com/2009...
Mike Chelen, Andrew Lang, Dan Hagon and 6 other people liked this
Downloaded from Oxford and installed OK for me under Vista. Data download for the paper was (unsurprisingly) slow on home wifi and browser (Ff) failed to close on first attempt but eventually up and running without problems. Slightly sad that we are back to ugly frames but otherwise nice (this from someone who is not a structural biologist).
- Peter Miller
Hope to see similar animation capabilities soon for other visualizations (particularly imaging data), as described for Adobe PDF files at http://www3.interscience.wiley.com/journal... and for TeX-based PDF at http://www.ctan.org/tex-arc... .
- Daniel Mietchen
sounds just great, for attribution matters, how will reference to a certain point in such a process work? http://ff.im/8HPXx
- Claudia Koltzenburg
@JC Downloaded the patch to run on my XP OS with no glitches at all.
- Graham Steel
I didn't have problems with the helper app but a little worried that the whole thing seems heavily dependent on what seems to be proprietary code. Why not use protein explorer?
- Cameron Neylon
Why does an Open Access journal use Closed technologies??
- Egon Willighagen
My hands are itching in making a Open solution for this...
- Egon Willighagen
The authoring component also costs which will limit its educational use too.
- Peter Miller
+1 Egon - we're working with a couple of computer science students to do just that.
- Andrew Lang
Bora has a video which could help those with trouble downloading the plugin see what this is about http://everyone.plos.org/2009...
- Jean-Claude Bradley
ok - got it to work finally. Works as advertised. It feels a lot like Jmol - Egon is that what you would use for an Open solution? It is a bit surprising that PLoS ONE went with a non OA solution. Bora can you disclose the reasoning? Is there really no free authoring component?
- Jean-Claude Bradley
It worked ok for me but crashed on exit.
- Andrew Lang
Science Discovers 32 New Planets... And Monty Python's Seen Them All - http://moviesblog.mtv.com/2009...
Searching for Earth-like planets explained by Eric Idle.
- Andrew Lang
What a Response to the Wolfram|Alpha iPhone App! - http://blog.wolframalpha.com/2009...
Mike Chelen liked this
The mobile browser works just fine for most needs.
- Andrew Lang
cool - are they still thinking about including some of our solubility data?
- Jean-Claude Bradley
£29.99? Seriously?
- Simon Cockell
I haven't heard back from them regarding the solubility data. I'll follow up later this week if I don't hear anything.
- Andrew Lang
@Simon. I was disappointed that they're going to charge for their API too but it is the business model they're going for right now - can't blame them - I'm sure it has cost them a lot of money to get as far as they are now.
- Andrew Lang
@Andrew - It is disappointing. I do get why, but I'm not sure £30 is the price point that's going to maximise their return. Especially given the pretty rigorous environment of the App Store (and the fact a free version of essentially the same tool is sitting behind the icon labelled 'Safari'). Charge £2.99, sell 20x as many copies... (http://www.techcrunch.com/2009...)
- Simon Cockell
What Are The Chickens in Your Life? - http://acscareers.wordpress.com/2009...
chickens and career changes
- Jean-Claude Bradley
As a youth I worked at a battery chicken farm collecting eggs - I only lasted a month. Put me off both eggs and chicken for years.
- Andrew Lang
Working on a dairy farm put me off milk for a long time too.
- Jean-Claude Bradley
Mice navigate a virtual reality environment - http://scienceblogs.com/neuroph...
Peter Miller liked this
Of course the next step is to put a cat on another controller and set up a virtual deathmatch. I wonder if they can learn to use the Quake weapons?
- Jean-Claude Bradley
I'm sure they could be trained to use weapons, maybe other stuff too - maybe we could use mice for crowdsourcing - mousesourcing?
- Andrew Lang
All kidding aside it would be cool to play Quake against mice. They don't seem to be harmed by running in the maze. Of course I'll be playing the side of the cats :)
- Jean-Claude Bradley
The Open Dinosaur Project - http://webapps.oru.edu/new_php...
Mike Chelen and Jean-Claude Bradley liked this
I helped some of my students enter some data.
- Andrew Lang
what a great project
- Jean-Claude Bradley
500 and beyond! - http://opendino.wordpress.com/2009...
Jean-Claude Bradley liked this
Mentions my latest ORU blog post.
- Andrew Lang
nice!
- Jean-Claude Bradley
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