Wikipedia:WikiProject Chemistry/IRC discussions/5 May 2009


 * [17:01:04]  Hi
 * [17:01:17] Hello! Glad you were able to join us!
 * [17:01:26]  Hi Alex
 * [17:01:33]  I have Gyorgy Pirok with - Hi Tony
 * [17:02:19]  Unfortunately Gyuri needs to get out by 17.30, so I want to get the best from him before he goes
 * [17:02:46] Gyuri is the technical guru, is that correct?
 * [17:02:58]  yes CTO, former wet chemist
 * [17:03:13] Is he sitting next to you, or will he log in under his own name?
 * [17:03:25]  he is here with me
 * [17:03:31] OK, let's get started
 * [17:03:38] Beetstra, are you there?
 * [17:04:34] Firstly, thanks a lot for the offer of help! Referring to my email last week, to which you gave some very nice replies.
 * [17:04:59] We asked for
 * [17:05:01] 1. Software to allow us to convert our "database" information (structure,
 * [17:05:03] name, formula, InChI, CAS No, etc.) between Excel, XML and SDF.
 * [17:05:28] I believe ChemFolder from ACD labs can do things like this, but it's expensive. Can your tools do this?
 * [17:06:08]  Just FYI CHemFOlder for academics is $500 I believe (or used to be). Not expensive
 * [17:06:21]  But Instant JChem is free to academia
 * [17:06:47]  yes, either staying in Excel (Jchem for Excel) and handling there or export to tab separated file.
 * [17:06:52]  all this is free for academics
 * [17:07:07]  everything is free for academics including forum support
 * [17:07:19]  as it is free for open websites
 * [17:07:40] http://www.chemaxon.com/product/ijc.html
 * [17:08:01] Can you tell us what the limitations are, compared to ChemFolder?
 * [17:08:01]  JChem for Excel is launched at the end of the month
 * [17:08:53]  not really, but we are probably better for chemical structure handling - we are enterprise toolkit CSoft arn't really
 * [17:09:10]  ChemFolder is not CSoft
 * [17:09:17]  also we provide API - and the performance of the desktop stuff will be exactly the same as with the server stuff
 * [17:09:44] <Alex_Allardyce> oops then I withdraw, perhas Tony knows better how we compare with ACD
 * [17:11:17] <Alex_Allardyce> but you can always try it and tell us
 * [17:11:21] <ChemSpiderman> Instant JChem is much more powerful in terms of flexibility, especially for programmers.
 * [17:12:21] <ChemSpiderman> ChemFolder was built with a specific purpose of databasing structures and reactions
 * [17:12:26] <Alex_Allardyce> I want to ask - we should separate the inhouse use - ie you guys moving files around with the server performance/programming - ie how 'any' wikipedia user will experience.
 * [17:13:15] <Alex_Allardyce> For inhouse (desktop) INstant JChem is very good but to cause least disturbance JChem for Excel would be useful also.
 * [17:14:04] <ChemSpiderman> ACD/Labs does not have a "For Excel" tool
 * [17:14:17] <Alex_Allardyce> For the site (server side) it is API and uses exactly the same classes - so the results are exactly the same
 * [17:14:33] As I understand it, all of this work is normally done offline on one's desktop, then once we have converted the file to the new format, we upload it into a repository for others to access.
 * [17:16:57] <ChemSpiderman> what are we trying to achieve today?
 * [17:17:04] <Alex_Allardyce> Can be offline or online - both Instant JChem (IJC), and JChem for Excel (JC4XL) can work on the desktop or on a remote database. So you can edit the repository live, tho you would proababnly want to assign rights so you do not have novices deleting the shared repository
 * [17:17:44] We want to find how best to use the offer of help from ChemAxon.
 * [17:18:05] <ChemSpiderman> ah-ok. Is there anyone else online who will be using these tools?
 * [17:18:10] <Alex_Allardyce> Gyorgy here now
 * [17:18:26] <ChemSpiderman> Other than ChemAxon staff, Martin and I..anyone else there?
 * [17:18:32] Ali_as isn't here, unfortunately. We will definitely try this out once the Excel version comes out – this is a critical need for us.  We'll let you know how things go! My other main question
 * [17:18:42] Physchim62: are you around?
 * [17:18:51] SOrry, that wasn't it!
 * [17:19:17] We are very interested in getting Wikipedia chemistry into the "semantic web"
 * [17:19:49] That means embedding InChIKeys as metadata inside structure drawing files
 * [17:20:34] It means finding ways to tag reactions so these can be found by web searches (unfortunately, there are no standards for reactions, no "InChI for reactions" yet
 * [17:21:20] Do you have any ways you could help us make Wikipedia Chem more chemistry-searchable, and more easy to reach via external searches?
 * [17:21:34] <Alex_Allardyce> OK there are a few question here
 * [17:23:32] <ChemSpiderman> ???
 * [17:23:36] <Alex_Allardyce> Alex again. Simple answer is yes. But to break down the issues I see. 1. Inhouse production (how to build and manippulate structure files). 2. online (user) structure search. 3. Reaction recognition/clustering
 * [17:24:05] FYI: We were working with ACD Labs on the first item, but things reached an impasse; I hope to push them on that this summer.
 * [17:24:48] <ChemSpiderman> I guess all the good guys left :-)
 * [17:24:54] <Alex_Allardyce> inhouse production. From what Martin has said this should be strightforward. Either using IJC or JC4XL for working with files and ALSO some API to manipulate the chemical file.
 * [17:24:56] Good breakdown - all of these would be good things for us
 * [17:26:39] <Alex_Allardyce> 2. online user search. See these example we provide in the distribution (which would be your basis). I would say that this is the core business for CXN and it's clients
 * [17:27:04] <Alex_Allardyce> AJAX code example/demo: http://www.chemaxon.com/jchem/examples/ajax/index.html
 * [17:27:19] <Alex_Allardyce> jsp implementation: http://www.chemaxon.com/jchem/examples/db_search/index.jsp
 * [17:27:54] <Alex_Allardyce> but there are other ways to achieve wthis aim, the idea is that it is how you want to implememnt and the API/toolkit approach lets you get there
 * [17:28:54] <ChemSpiderman> Looking at the Ajax page...
 * [17:29:11] <ChemSpiderman> Hangs in Firefox after scrolling. Is it for IE only?
 * [17:29:25] <ChemSpiderman> Oops...no...its back again
 * [17:29:31] <Alex_Allardyce> for point 3. you can search for reactions by the transformation and find reactions by a generic transformation query or finsd similar reactions to a given input. There is also the potential to use clstering - but we have not tried this yet
 * [17:29:32] <ChemSpiderman> now scrolling.
 * [17:29:50] <ChemSpiderman> Wikipedia doesn't have ANY mapping in the reactions. They are images
 * [17:30:17] ChemSpiderman: You're right - but I'd like to change that if possible!
 * [17:30:22] <ChemSpiderman> they are not reactions...they are images of reactions. Every one would need to be redrawn with mapping
 * [17:30:37] But we have to start somewhere
 * [17:30:55] <Alex_Allardyce> trickey, we have no image recognition technologies, (tho the toolkit approach does leave you free to mix and match whatever is out there)
 * [17:31:21] <Alex_Allardyce> Also you can store reactions in a smiles format as you would do with molecules
 * [17:31:31] <ChemSpiderman> ALex..look at record 2021 on that link http://www.chemaxon.com/jchem/examples/ajax/index.html
 * [17:31:53] <ChemSpiderman> am I seeing hexavalent carbons?
 * [17:32:22] <ChemSpiderman> small point..but you likely have some structure cheking tools under the standardizer to catch things like that?
 * [17:32:30] <Alex_Allardyce> or store in any format you want really: http://www.chemaxon.com/marvin/help/formats/formats.html
 * [17:33:32] Between myself, v8rik, Rifleman and K we could put together quite a database of reactions that have been uploaded, and build on that foundation
 * [17:33:53] <ChemSpiderman> I think your tools can help Wikipedia...it will need rework of images to reactions to create the database but it is feasible
 * [17:34:08] <Alex_Allardyce> yes for sure, this can be caught either with Standardizer or API. Also there is a new tech we just launched called structure checker which will pick up errors in chemical files for molecules and reaction and you can automatically fix the file using optional 'fixer'
 * [17:34:50] <ChemSpiderman> WP will need someone to lead the cheminformatics efforts or you guys will be providing a lot of support. Martin, how will the Wiki Foundation be with integrating an external app in for searching?
 * [17:34:56] Those Wikipedians could provide ChemDraw files or similar for all their reactions. If we put in our MOS that reaction files are to be handled as some kind of diff, most future reactions would then go into that format
 * [17:35:06] <Alex_Allardyce> We are going to loose Gyuri - I can continue but this process is quite slow and counter intuitive. Can I invite you guys to a webex soon and we can see this
 * [17:35:24] Thanks Gyuri!
 * [17:35:42] <ChemSpiderman> I agree...IRC is very uncomfortable. Even a multi party Skype is much better
 * [17:35:49] <ChemSpiderman> Bye Gyuri
 * [17:36:02] <Alex_Allardyce> (Gyuri here) cheers and glad this is live on wikipedia. speak later
 * [17:36:25] We'll try out the major tools and then talk again once we're familiar with them
 * [17:36:53] <Alex_Allardyce> Try instant JChem, it should not be new to the old ISISBase user
 * [17:37:43] Alex_Allardyce: I last used MDLBase on a Vax in VMS, with a scroll wheel instead of a mouse!
 * [17:37:53] But I use IsisDraw all the time
 * [17:38:25] ChemSpiderman: I think the Foundation will resist such changes, but if we get our grant, then we can (in effect) do it ourselves
 * [17:38:42] <ChemSpiderman> gotcha
 * [17:38:59] <Alex_Allardyce> ok then OK for you Martin. There are resources to help the others and I ask you send me a mail aa__at_chemaxon.com and I can send you a license to fiully enable (the Personal edition is free but limited)
 * [17:39:01] Once the hard work is done to integrate it with full security, then the Foundation may be OK about implementing it on WP
 * [17:39:39] Alex_Allardyce: Thank you very much!
 * [17:39:54] <ChemSpiderman> see you Alex
 * [17:40:12] <Alex_Allardyce> Is there anything stopping us meeting on webex and reporting here?
 * [17:40:23] I'm in my last week of the semester so I probably won't be able to do anything for a couple of weeks, till after my marking is done etc.
 * [17:41:01] Alex_Allardyce: No problem at all. If it's totally open & public, the normal place to report would be on-wiki
 * [17:41:54] Hi NormWork! The ChemAxon people are just finishing up
 * [17:42:07] <Alex_Allardyce> then lets arrange a time and we can discuss/show better. there is quite a range of topics here and bleed confusion is probable
 * [17:42:26] What is "bleed confusion"?
 * [17:42:38] <NormWork> walkerma: Nice!
 * [17:43:15] <Alex_Allardyce> bleed is when one colour mixes with otnother colour during a printing process -- ending up (normally) with a mud brown colour that is useless - I just made up the term
 * [17:44:11] So we might confuse the various topics, right?
 * [17:44:46] <Alex_Allardyce> yes - inhouse use, online use, molecules, excel, XML, taging, there are a few primaries there
 * [17:45:22] Normally we tend to focus on one or two very specific things on IRC (or we TRY to!), to avoid that - but this was our first meeting with you, and we only had a short time, so I wanted to put everything on the table.
 * [17:46:40] <Alex_Allardyce> Sure and good, I think we understand - but we do this all day so we should. But as Martin mentioned there is not a huge amount of informatics experience here (except probably Tony) so there is a need to ground the topic anyway
 * [17:47:16] OK, we'll report back once we've tried things out. At the end of May I will be working on the chemical identifier/CA validation process again, so I'd be using Instant JChem for Excel a lot for that.
 * [17:47:31] <Alex_Allardyce> what I don't want is a lack of delivery and worse, wasted development effort
 * [17:47:53] <Alex_Allardyce> Just to correct - Instant JChem is one product and JChem for Excel is another (not yet released)
 * [17:48:20] <Alex_Allardyce> :)
 * [17:48:20] Certainly not! I think ali_as (not here today) and Physchim62 will also be heavily involved with that work.
 * [17:48:37] OK, thanks for clarifying
 * [17:49:20] <Alex_Allardyce> Good, glad that there are developers.
 * [17:49:51] Beetstra is a chemist with strong developer experience; DMacks is also very good, and Physchim62 can do some as well
 * [17:50:10] But ChemSpiderman is our main informatics person
 * [17:51:44] <Alex_Allardyce> Then you will do well, knowing how much can be done and how to do is most of the job - especially with innovative aims
 * [17:52:16] <Alex_Allardyce> OK - I await a ping from Martin to arrange a webex or at least a phone conversation with the interested partiers. I would suggest the result of this is a description we agree on then we can comment on each task separately (by irc)
 * [17:52:55] <Physchim62> I'll be with you in 10–15 mins (teaching at the moment)
 * [17:53:06] I'd like to get familiar with JChem first - so that ping may be in a month or so, OK?
 * [17:54:31] <Alex_Allardyce> ok, I send an all product license, if anyone else wants to try this out then again email is above
 * [17:54:52] Is there anything else before you go?
 * [17:55:00] * Beetstra reads back
 * [17:55:14] <Beetstra> Do I understand correctly this is mainly reactions, not compounds only?
 * [17:56:16] No, we've been discussing both
 * [17:56:18] <Alex_Allardyce> AA - no both, and fairly well (if I say so myself)
 * [17:57:21] <Alex_Allardyce> If I can help any of you with this please do ping me. We believe in web chemistry so are v. interested in wikipedia's interest
 * [17:57:32] <Alex_Allardyce> Look forward to your contact. Cheers
 * [17:58:07] Thanks a lot for your time!
 * [17:58:23] <Beetstra> I have never involved myself too much with reactions on wiki, we don't have a decent box for it I believe, compounds are easier in that respect
 * [17:58:36] <Alex_Allardyce> bye
 * [17:58:42] <Beetstra> bye Alex_Allardyce
 * [17:58:48] <ChemSpiderman> bye ALex
 * [17:58:59] <--| Alex_Allardyce has left #wikichem
 * [18:00:21] Beetstra: I'm not just thinking about specific articles on reactions on WP, I'm thinking about all of our examples, such as those found at
 * [18:00:23] http://en.wikipedia.org/wiki/Copper(I)_chloride#In_organic_synthesis
 * [18:00:49] <Beetstra> Hmm, yes. true
 * [18:01:00] <Beetstra> But maybe even more difficult
 * [18:02:09] I would like to embed metadata behind the images, so that someone could (potentially, at least) find a 1,6-addition using a Google search.
 * [18:02:44] <ChemSpiderman> what search would they do on Google to get that?
 * [18:03:00] Obviously, the same applies to specific compounds, in which case the metadata would be an InChIKey
 * [18:04:01] <Beetstra> what I mean, walkerma, is that I like the idea, and it is something we can think about (a little), but we still have the compounds. If we solve compounds, then reactions might follow easier.  If we now also include tackling reactions, we might get too much
 * [18:04:39] ChemSpiderman - right now, I don't know that there is anything. But that's where I would like to see us go, and I want to keep asking that question.  I've actually been asking the same question since 1996, and now there is some possibility of getting an answer!
 * [18:04:51] <Physchim62> Damn, missed Alex
 * [18:05:48] Beetstra - I agree, for now. The structure identifiers are much more doable.  But I want to make sure we don't go down a road in 2009 that makes it impossible to add reaction identifiers in 2011.
 * [18:06:39] I also want to get the seeds planted now, so when (say, in 2010) ChemAxon is adding a feature on reaction searching, they think - oh, this could be adapted to help the WP people! Let's add in a web feature!  Etc
 * [18:07:09] <ChemSpiderman> Wach out for impending reaction support on ChemSpider...
 * [18:07:10] I like to have a long term vision of where we want to be going, and personally that's something I see as very helpful for chemists.
 * [18:07:18] <ChemSpiderman> watch..
 * [18:08:10] That is partly, of course, because my research is in reaction methodology, and my job for 12 years was process R&D - designing reaction processes, not substances.
 * [18:08:21] <ChemSpiderman> we already have a couple of hundred organic synthesis procedures and it's growing. These will be mapped as reactions by the end of the year I hope
 * [18:08:44] ChemSpiderman - how will you map them? Will you use the MDL reaction format?
 * [18:09:00] <ChemSpiderman> yes
 * [18:09:08] Great!
 * [18:09:17] <Physchim62> is that semantic?
 * [18:09:19] <ChemSpiderman> and InChIReact definitions when they are available
 * [18:09:30] Unfortunately, that's proprietary, right?
 * [18:09:42] I meant the MDL format
 * [18:09:59] <Physchim62> I mean, March terminology is not really semantic for me, but it's the best attempt to create a systematic hierarchy of reactions that I've yet to see
 * [18:10:03] <ChemSpiderman> A derivative of the format is used by most vendors
 * [18:10:18] <ChemSpiderman> we haven't started yet of course.
 * [18:12:16] My PhD adviser (Jim Hendrickson) also devised a system that is quite widely known - you can see a lengthy description of it in Smith's Organic Chemistry book
 * [18:12:37] <ChemSpiderman> ok
 * [18:12:53] But that defines generic reactions - I'm looking for more specific ones than that, and I think for that you need the MDL system, probably
 * [18:13:50] But Jim is currently writing his masterwork - a complete summary of his life's work, one unified description of all organic reactions. I'll let you know when his manuscript is ready!
 * [18:14:02] <ChemSpiderman> nice!
 * [18:14:06] He's 81 years old BTW
 * [18:14:19] <Physchim62> best he finish it quick then ;)
 * [18:15:34] His description of all possible pericyclic reactions (Angewandte, ca 1975) is brilliant, and allows you to come up with new reactions easily!
 * [18:15:53] <Physchim62> will the MDL system allow the specification of generic reactants, eg "alkyl halide"
 * [18:17:55] <Physchim62> ?
 * [18:17:56] <Beetstra> "unified description of all organic reactions" -> X -> CO2 -> Y -> CO2 -> Z ??
 * [18:18:32] That's an inorganic chemist's cynical view, I think!
 * [18:18:44] <Beetstra> heh
 * [18:19:07] <Physchim62> you won't get any other sort of view from us inorganic chemists! we have hearts of stone, you know ;)
 * [18:19:37] Just remember all those ligands you buy from Strem have to be made by some poor, underpaid organic chemist!
 * [18:20:02] <Physchim62> I made all my own ligands, thank you very much
 * [18:20:18] <Beetstra> I did some olefin polymerisation experiments in the past, making 20-30 gram of polyethylene in one run of half an hour .. I once said to an organic chemistry that I, in that 30 minutes, made more C-C bonds (2 Mol!) than many organic chemists make during a significant part of their career .. that is generally unliked
 * [18:20:25] <Physchim62> It was the only way the Boss could persuade me to learn some organic chemistry…
 * [18:20:30] <Beetstra> eh, 1 mol
 * [18:20:52] <ChemSpiderman> Do we have anything specific we are going to discuss today?
 * [18:21:12] <ChemSpiderman> I am interested in getting feedback on whether anyone is using the ChemBox builder?>
 * [18:21:18] BTW, a very useful website that uses Hendrickson's system is here: http://www.webreactions.net/
 * [18:22:08] <Physchim62> I'm not using it at present, but would do so in the future. My survey of chemboxes is coming along, but it's a long job
 * [18:22:32] <Physchim62> Beetstra, what are your plans for chembox development?
 * [18:22:36] ChemSpiderman, I will be doing almost no wiki chemistry until the end of May. I have too much chemistry to do with a red pen; also our (messy) lab is being refurbished this summer, and I need to clean it out by the end of May.
 * [18:22:48] <Beetstra> I did some work on the chembox, there is still some old rubbish around which needs cleanup (see WT:CHEM and the infobox talkpage)
 * [18:23:38] <Physchim62> Beetstra: have you any further plans beyond what's on those pages? I would like to revamp the coding and eliminate some obscure parameters
 * [18:23:42] <Beetstra> And I am planning to make CheMoBot 'create a chembox from scratch' (with the aim of being able to 'repair' verified data or at least tag it)
 * [18:23:44] <ChemSpiderman> The only issue I keep hearing is SVG. If that is it then I will leave it as is for now, add support of ACS formatting and choose SVG or PNG in the future and leave it for feedback. Is there a way to spread the message that it exists?
 * [18:24:00] I think this is not something that will suddenly get used hundred of times in a month, since most articles already have chemboxes; it is something that all of us will use a handful of times a month for the next 10 years+
 * [18:24:23] <Physchim62> It will be publicised, yes
 * [18:24:42] <Beetstra> No, no revamp ideas. Only that (which is just cleanup), and thinking about 'combining chembox and drugbox', though I am not worried about it for the future
 * [18:25:08] <ChemSpiderman> I am thinking especially of people creating NEW chemboxes. It is quite surprising to me how many organics we don't have linked from ChemSPider that are on Wikipedia/
 * [18:25:15] <ChemSpiderman> I add a few a night at present
 * [18:25:15] <Physchim62> My coding revamp would be "silent" on WP articles
 * [18:25:43] <Beetstra> ChemSpiderman, what is your experience with TIFF?
 * [18:25:53] Once you have the ACS settings done, publicise it at WT:CHEM and the infobox page, and maybe we can get it in the Signpost if we're lucky (perhaps combine it with a mention of structure searching)
 * [18:25:57] <ChemSpiderman> I prefer TGIF
 * [18:26:01] <ChemSpiderman> :-)
 * [18:26:12] <ChemSpiderman> Thank God its Friday...
 * [18:26:16] <Beetstra> Reason I ask: http://www.mediawiki.org/wiki/WMDE_contract_offers/Implement_full_support_for_TIFF_files
 * [18:26:27] <ChemSpiderman> Anyhow...TIFF isn't bad at all.
 * [18:26:56] <Physchim62> TIFF is big as a file format, but that doesn't seem to be a problem these days
 * [18:27:58] <ChemSpiderman> There are also various resolution levels as I recall.
 * [18:28:15] <Beetstra> Well, they are talking about 'extracting metadata', I wonder in how far they would be interested in mediawiki for that on other files
 * [18:28:27] <ChemSpiderman> Yes..just checked ChemSketch ...we offered a choice as to resolution
 * [18:29:12] <ChemSpiderman> Martin...you talked earlier about wanting InChIs embedded in images. I did that 2.5 years ago at ACD/labs in ChemSketch. Did people use it?
 * [18:29:15] But our standard right now is PNG or SVG (depending who you talk to) - so we should support one of these, unless TIFF is about to completely take over. If you can get high quality SVG, that is probably the best thing to go for.
 * [18:30:06] ChemSpiderman - the problem is that it didn't work well. We got (for example) one InChI even when a reaction was uploaded - it treated the complete reaction as if it were one compound
 * [18:30:25] <ChemSpiderman> ah-ha
 * [18:30:29] <Physchim62> so it needs to be optional
 * [18:30:30] When I followed up with Greg Pearl, he suggested waiting to see if InChIKey was fully adopted.
 * [18:30:31] <ChemSpiderman> I was focused on compound box support
 * [18:31:04] Which is a great idea. But then Greg got replaced by Mark, then Mark has moved on himself, etc!
 * [18:31:27] I was planning on raising the topic again this summer, now that InChIKey has become more "official"
 * [18:32:05] <ChemSpiderman> sorry on phone...back soon
 * [18:32:20] <Physchim62> OK, so we propose to whoever matters at ACDLabs these days that they make InChI embedding optional, with default yes for single fragment files and default no for multifragment files
 * [18:32:30] The original setup wasn't robust enough, and apparently it wasn't a trivial problem to get it to work properly
 * [18:32:52] We need them to see it as a priority
 * [18:33:36] I also spoke to people at CambridgeSoft in March, and they were interested too - that would be great, since ChemDraw is the clear market leader.
 * [18:33:36] <Physchim62> ChemSketch can count fragments, that's not a problem: we need to define what we (WP/WM) want!
 * [18:35:21] Maybe we should work on that question over the next week or two, email any proposals we have to each other, then discuss the topic in a fortnight's time? I'm giving my final exam at this time next week, BTW, and this is a discussion I'd really like to participate in.
 * [18:35:47] I think PC has phrased the task very nicely
 * [18:36:30] <Physchim62> What I would like to hear from other is how this metadata should be formatted: that way, we can propose a "WikiMedia standard"
 * [18:37:22] Once we have a formal proposal, we can maybe check with Tim Starling or someone
 * [18:37:43] <Physchim62> we would need to check with Leyo first!
 * [18:37:44] Can someone talk with the German wikichemists, to get their views?
 * [18:38:14] <Physchim62> I will blog on it this evening
 * [18:38:48] <Physchim62> I think this needs to be something that goes beyond WP/WM, even if we are the driving force
 * [18:40:16] My hidden agenda - if we can get subliminal InChIKeys embedded into every ChemDraw structure that gets put onto the web, then "bing!" you have a structure-searchable web
 * [18:41:06] Put that together with some substructure tools on ChemSpider, and you have some VERY powerful chemistry search tools on the web.
 * [18:41:18] <Physchim62> yes, but beware of the "multiple fragment" problem!
 * [18:41:40] <Physchim62> that's why we need to specify a format
 * [18:42:52] <Physchim62> let's get a format together for single-fragment structures, then work from there: FGS, we were talking about it in Paris 18 months ago!
 * [18:44:42] Physchim62: Yes, but we are only a handful of people, with day jobs! We're moving forward on other fronts too, remember.
 * [18:45:16] <Physchim62> yes, I need to earn some money as well (done €20 today, I'll survive on that)
 * [18:47:16] OK, we have two weeks to transform the world of chemical information and lay down complete new standards. Meanwhile CSM will start compiling the world's largest reaction database in his spare time.  Is there anything else we need to cover today?
 * [18:49:51] <Physchim62> I would add that PNG doesn't support Exif, so yes, we actually are on the path to world revolution…
 * [18:50:32] <Physchim62> don't forget to stop off for kebab and chips on the way 'cos you never know when you'll next get the chance :P
 * [18:51:27] Potsdam doesn't have a kebab and chip shop, unfortunately - but I'll pick up a burger and fries instead
 * [18:52:09] <Physchim62> If you ask them to cut the burger into thin slices, you'll get the same effect…
 * [18:53:33] <ChemSpiderman> I'm back and have a question...
 * [18:54:12] <ChemSpiderman> what is the chance, and when could it be, that we could get 3-4 of us around table for a solid day of discussions about what WikiChemistry needs in terms of cheminformatics?
 * [18:55:22] What sort of table?
 * [18:55:32] <ChemSpiderman> If there is an international conference where we can gather I'd fly in to sit and discuss WIkiChem needs and then we should find the partners to help make it happen
 * [18:55:50] <ChemSpiderman> Walnut Maple
 * [18:56:05] A virtual table? An IRC, Skype, or a conference call?  Oh yes, I love Walnut
 * [18:56:32] <ChemSpiderman> I'd prefer a table...face to face. I know it's a challenge but it's not impossible
 * [18:56:42] There is the Wikimania conference in Buenos Aires in August - PC and I are hoping to go, but not totally sure yet
 * [18:57:08] I worked out, though, it'd be cheaper for me to go to that than it was for ACS in Salt Lake City!
 * [18:57:13] <Physchim62> Wikimania is the best bet: I have no other plans to cross the Atlantic
 * [18:57:28] <Physchim62> and I'm not really on the international conference circuit
 * [18:57:44] <ChemSpiderman> what dates in August? I am already in the UK for a week and in Washington for a week that month
 * [18:57:56] <Physchim62> end of August 26-29 I think
 * [18:58:00] The other obvious thing would be the IUPC meeting in Glasgow - if you want a table made from steel girrderrs
 * [18:58:16] <ChemSpiderman> I am going to the IUPAC meeting in Glasgow...
 * [18:58:17] <Physchim62> when's IUPAC?
 * [18:58:29] But I think I'd selected Wikimania as being more affordable
 * [18:58:48] And also, it's about time I went to another wiki conference
 * [18:59:12] http://www.rsc.org/ConferencesAndEvents/RSCConferences/IUPAC2009/
 * [18:59:17] <Physchim62> I can't go to Wikimania without sponsorship, but I could do Glasgow
 * [18:59:26] 2-7 August
 * [19:00:12] <Physchim62> Wikimania is 26–28
 * [19:00:15] £265 registration
 * [19:00:19] for IUPAC
 * [19:00:34] Wikimania is free registration I think
 * [19:00:34] <Physchim62> fuck that for a lark
 * [19:00:50] <Physchim62> it's not free, but bursaries cover it
 * [19:01:50] <Physchim62> I could try to arrange to be in Glasgow at the time of the IUPAC conference, and meet up with whoever else is there
 * [19:02:03] <ChemSpiderman> Works perfectly for me
 * [19:02:23] <Physchim62> OK, I will need to discuss it with the Boss!
 * [19:03:22] <Physchim62> she wants to spend August in an English-speaking country, but she might be willing to pass by Glasgow
 * [19:04:15] <walkerma_> CSM: Are you planning on visiting upstate NY any time soon? The two of us could at least get around a table - we have a nice plastic one, under the shade of a lot of fruit trees coming into blossom soon
 * [19:04:43] <ChemSpiderman> it's possible that we will be up to visit family in July and I can hop over for an evening if I do.
 * [19:04:56] <ChemSpiderman> we can put something cool on that table...
 * [19:05:06] <ChemSpiderman> wet and cool
 * [19:05:44] <Physchim62> the mind boggles :P
 * [19:05:51] <walkerma_> BTW, PC, I wanted to go to the Fluorine conference this year, but it would cost me around $3000. It's around $600 to register, $200 a night to stay at the resort hotel (nothing else near) and probably $1000 to fly there... I decided Buenos Aires was cheaper
 * [19:06:38] <Physchim62> I know, that's why I'm no longer on the conference circuit. Pure corruption, the lot of it
 * [19:07:42] <Physchim62> a bit like the subscription rates for scientific journals
 * [19:08:12] <walkerma_> ChemSpiderman: OK, that sounds good; I will probably be away a few days in early July. The blossom will be gone, but you're very welcome to come and stay!  I think we could cover a lot of ground, and we could start writing the grant proposal too.
 * [19:09:07] <Physchim62> The Boss wants to visit Montreal at some point, but I'm trying to put it off for this year…
 * [19:09:16] <walkerma_> (Student here, I should go soon, though I have a few minutes to close)
 * [19:09:30] <walkerma_> Montreal is only an afternoon's drive from here!
 * [19:09:44] <Physchim62> I know, I'll let you know if we're in the area
 * [19:09:57] <Physchim62> but don't count on it this year
 * [19:10:39] <Physchim62> "economic crisis" and all that!
 * [19:12:33] <Physchim62> anyway, if Antony is going to Glasgow, I will try to get myself to the city if not to the conference.
 * [19:13:44] <ChemSpiderman> I will be there for sure
 * [19:14:27] <NormWork> Hey,the photo of copper(1) chloride is severely degraded!
 * [19:14:29] <walkerma_> I just got the license info from Alex, I'll let you know how it looks
 * [19:14:48] <Physchim62> OK. You're both welcome in Barcelona!
 * [19:15:24] <walkerma_> Normwork, which picture? Or do you mean the CuCl is a bit oxidised?
 * [19:15:30] <NormWork> I do.
 * [19:15:34] <NormWork> It's olive green.
 * [19:15:35] <Physchim62> NormWork: it's been sitting on Wikipedia for too long!
 * [19:15:44] <NormWork> Ah, of course!
 * [19:16:23] <walkerma_> Can we get Beetstra to write a bot to put an Argon atmosphere round things? That explains why our articles on alkyllithiums are so crap, as well
 * [19:16:47] <Physchim62> I actually think it's a good image: that's what oxidized copper(I) chloride looks like! but you're right, it should have a caption
 * [19:17:25] <NormWork> Sorry for the lateness, work is interfering with my irc.
 * [19:17:35] <Physchim62> we have plenty of pictures of pure white powders that we could pretend were cuprous chloride, but no chemist would believe us!
 * [19:17:47] <walkerma_> Actually, I got a brand new bottle of CuCl in 2005 or so, and this is what it looked like straight out of the bottle:
 * [19:17:48] <walkerma_> http://en.wikipedia.org/wiki/File:Copper(I)_chloride.jpg
 * [19:18:37] <Physchim62> my point exactly!
 * [19:19:16] <NormWork> walkerma_: Then the photo is valuable information, but it needs to say something like "send this crap back to vendor"
 * [19:19:54] |<-- walkerma has left irc.freenode.net (Read error: 110 (Connection timed out))
 * [19:20:49] <walkerma_> OK, I think I'll have to go
 * [19:20:57] <walkerma_> Any other things before I go?
 * [19:21:09] <Physchim62> NormWork: not at all, any vendor would sell you CuCl like that, unless you paid them ten times the market rate
 * [19:21:21] <NormWork> I think that's one of the reasons that copper(I) iodide is used as often as it is. It't doesn't degrade as easily.
 * [19:21:24] <Physchim62> I have to go pretty soon too
 * [19:21:53] <Physchim62> is the degradation important in the organic reactivity of CuCl?
 * [19:22:06] <NormWork> Short answer: yes.
 * [19:22:16] <Physchim62> OK!
 * [19:22:28] <NormWork> It causes reduced yields, and more troublesome, it causes unexpected byproducts.
 * [19:22:44] <Physchim62> in which case, prepare your own!
 * [19:22:45] <NormWork> Copper(II) coupling reactions.
 * [19:22:53] <NormWork> That's the right answer, too.
 * [19:23:29] <NormWork> My problem has just been with students who a) don't know, and b) use the stuff from the vendor.
 * [19:23:52] <NormWork> So my comment is salient: THe picture is valuable,and needs some explanation, including in the text.
 * [19:24:04] <Physchim62> if it's that important! many commercial materials are unsuitable for research, simply beacuse PhD students are cheaper than industrial technicians to purify the small quantities required
 * [19:24:15] <walkerma_> NormWork: Good point!
 * [19:24:42] <NormWork> I can't get to it this morning, but maybe this evening.
 * [19:25:30] <Physchim62> I must dash, if you could add the necessary detail NormWork that would be great
 * [19:26:28] <walkerma_> OK, must go too. Cheers!