Google now indexing thumbs. Final page of solubility book: Solubilities of inorganic and organic compounds: a compilation of ..., Volume 1 By Atherton Seidell
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
@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
"...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
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
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
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
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...
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- Jean-Claude Bradley
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
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
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
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
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
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...
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- 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
“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
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
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
@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
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
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
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