Antony Williams › Likes

Victor / Mendeley Team
Join us for “Mendeley for Life Scientists”, a free online instructional session on July 7th at 1PM EDT -
Dislike for GotoMeeting use... - Egon Willighagen
What's wrong with GotoMeeting? - Antony Williams
No Linux support. We're moving to WebEx Event Center, as it looks like it might work for us. We've been looking at a number of options, such as Adobe Connect (it's way too expensive for the number of attendees we have) and finally settled on WebEx as it works on Linux and supports the features we need for a comparable price. Haven't fully tested it yet, though, but pretty sure we'll be... more... - Mr. Gunn
Andrew Lang
Modeling question. Why would you use principal components as descriptors instead of the descriptors themselves?
because PCA can be viewed as a dimension reduction method, so if you don't know which N of M descriptors to choose (M being large) the hope is that the first N PC's will contain the informative descriptors. - Rajarshi Guha
depends on other things... in case of multi linear regression, it's a must to get (somewhat) stable models... it addresses co-linearity between original descriptors - Egon Willighagen
I wouldn't say PCA is a must. It's just a way to get fewer descriptors - Rajarshi Guha
What's the drawback? You can't measure the importance of individual descriptors? - Andrew Lang
your coefficients gets messed up, because any linear combination will work... coefficients for descriptors can easily swap from positive to negative, resulting in multiple interpretations. e.g. xlogp increases Foo, while in another model is decreases that same Foo - Egon Willighagen
People use it because they don't understand quite what it's doing. I'd go a bit further than Rajarshi, and say that there is no reason to do it. If your descriptors have no variance in your dataset, toss them out. If they don't have any correlation with the activity toss them out. Why should the PC1 be correlated with activity? Note that if you don't scale your descriptors to the same ranges, using PC is very suspect. - Noel O'Boyle
Bill Hooker
Tags: opendata open.pharma collaboration drugdiscovery - Bill Hooker
Jean-Claude Bradley
Bill Hooker
CiteULike: How Informatics Can Potentiate Precompetitive Open-Source Collaboration to Jump-Start Drug Discovery and Development -
Tags: collaboration precompetitivesharing drugdiscovery opendata openscience - Bill Hooker
looks interesting Bill - do you have the pdf? - Jean-Claude Bradley
Bill, did you also see this one: ? - Egon Willighagen
Yep, just sent you a copy (to your gmail address). - Bill Hooker
Pierre Lindenbaum
RT @wjjessen: China's BGI pumped out 500Tb of genomics data in 2010, 10x amount produced by US NCBI in the past 20yrs!
what do they do with it? - Rajarshi Guha
Jean-Claude Bradley
Egon Willighagen
Linked open drug data for pharmaceutical research and development -
Journal of Cheminformatics, Vol. 3, No. 1. (2011), 19. There is an abundance of information about drugs available on the Web. Data sources range from medicinal chemistry results, over the impact of drugs on gene expression, to the outcomes of drugs in clinical trials. These data are typically not connected together, which reduces the ease with which insights can be gained. Linking Open Drug Data (LODD) is a task force within the World Wide Web Consortium's (W3C) Health Care and Life Sciences Interest Group (HCLS IG). LODD has surveyed publicly available data about drugs, created Linked Data representations of the data sets, and identified interesting scientific and business questions that can be answered once the data sets are connected. The task force provides recommendations for the best practices of exposing data in a Linked Data representation. In this paper, we present past and ongoing work of LODD and discuss the growing importance of Linked Data as a foundation for... - Egon Willighagen
DOI is broken ... - joergkurtwegner
DOI is just slow with catching up... :( direct link: - Egon Willighagen
still waiting for my trial code for triplemap :) - Jean-Claude Bradley
Maybe I can help... ... I sent an email. - Egon Willighagen
Thanks Egon - got it working - Jean-Claude Bradley
Matthew Todd
Discussion about how best to link data (here NMR) to online lab book (Labtrove). Pls chip in.
Thanks to!... for starting - Matthew Todd
JSpecView and Rich' HTML5 stuff mentioned... - Egon Willighagen
I added what we do in the ONSC lab notebook pages and the - Andrew Lang
Thanks all. Am using the etherpad for all comments atm - Matthew Todd
Heather Piwowar
.@ChemConnector Agreed! #figshare deposits are useful non-traditional research output, worth tracking. #altmetrics would be great fit.
Spoke to Jason Priem about getting something like this going but he hasnt the time right now. Anyone know who else we could speak to about getting this implemented. Heather? - science3point0
Nope, not sure. Guessing something based on a google search would achieve the lowest hanging fruit right now. I'm guessing more customized tools will emerge for datasets etc in the next year or so... these can then be customized for figshare. - Heather Piwowar
Depends on what you want to track really. We might be able to do something with a current project but its not going to solve the whole problem by any means... - Cameron Neylon
Very intrigued @Cameron, will/can you divulge any more? You have my email if its hush hush, although I didnt think you did hush hush :) - science3point0
Heather Piwowar
Do you currently include datasets on your CV as research outputs? How about open source software?
My code is listed in a separate section on my CV directly below the publications. - Dan Gezelter
Egon, data and code both? - Heather Piwowar
Data not yet. I do not have much data to offer myself yet. I'm a data sink, not a data provider. - Egon Willighagen
If comfortable, pls share links to CVs that list datasets. Might appear in slides at some point, if you don't mind? :) - Heather Piwowar
My online CV doesn't really look like a CV -> - Egon Willighagen
Useful for code, thanks Egon. Interested in lots more too! - Heather Piwowar
I would include both -- if I had any to include, which, sadly, I don't. I'd be interested to hear from anyone who has these things but *doesn't* add them to their CV -- why on earth not? - Bill Hooker
I guess I'll answer that one. I'd never seen anyone else add them to their CV so a) I didn't think of it, b) I didn't think it was the done thing, and c) it wasn't immediately obvious where/how. At this point none of those things are true anymore so I plan to add them, I just keep not getting around to it. But I will Soon. - Heather Piwowar
I do recognize that adding them would take only about as long as it takes for me to comment on this thread. heh. - Heather Piwowar
I would add the dataset (because it is a research output), but if software is a tool (rather than a 'research') I would put it under 'contribution to research environment' (which is one of the portfolio headings in our standard assesment). - Kubke
As Heather said on twitter, a link to a FigShare account could include your research in aggregate. - science3point0
tony yuan
OLN - an ELN running on all platforms, including iPad and Android. It is free for Individual and Education users. Video 1:
OLN - an ELN running on all platforms, including iPad and Android.  It is free for Individual and Education users.  Video 1:
Noel O'Boyle
Announcing 2nd Open Babble - Pre-registration now open -
Announcing 2nd Open Babble - Pre-registration now open
Supplemental or detrimental? - The Scientist - Magazine of the Life Sciences -
Journals debate the value of supplemental materials -- Last November, Journal of Neuroscience abolished supplemental materials -- the extra figures and tables that appear online, but not in the printed version of a paper. Editor-in-chief John Maunsell argued in an editorial that the escalating amount of supplemental materials had begun to devalue the peer review process. - Joe
Maunsell sees the right problem, but draws the wrong conclusion. We need more data, not less, but the data itself should be publishable and citable, as opposed to needing to be shoved into "supplementary materials". With online publications, there's really no need for supplementary materials, but that's because the data should be included as part of the publication or a separate publication in its own right. - Mr. Gunn
Noel O'Boyle
Open Babel book now available -
Open Babel book now available
I just ordered a copy for myself! - Antony Williams
Getting a copy for the library! - Brian Westra
I will order one for our department being available at my desk - joergkurtwegner
Looks like being a best seller! :-) - Noel O'Boyle
Rich Apodaca
Ultra Fast substructure search based on the VF2 outperforms CDK UIT -
I wish he had just given the 12 substructure directly... :( - Egon Willighagen
Victor / Mendeley Team
Build an app with Mendeley data, make research more open, win $10,001! -
Kudos to the person(s) behind the marketing efforts at Mendeley! - Antony Williams
No official marketing department, Antony, just a bunch of us trying to spread the word however we can ;-) - Mr. Gunn
Jean-Claude Bradley
Validating Melting Point Data from Alfa Aesar, EPI and MDPI -
Validating Melting Point Data from Alfa Aesar, EPI and MDPI
1. I continue to be amazed that such a fundamental property as melting point contains so much confusion. 2. I wonder if Dryad could be convinced to open their doors to datasets that aren't (yet) attached to peer-reviewed papers, a sort of data-preprint-repository? Paging Heather Piwowar, Heather Piwowar to the thread please... - Bill Hooker
FigShare does this Bill. - science3point0
@Bill... nothing really new here, just another example. This problem is know in the field for a very long time by at least by me and a few peers. Solving the problem seems to be a serious challenge, noticing that after more than 16 years (when I noted these things as a student) nothing much has changed, despite the work of some, like the Blue Obelisk movement. - Egon Willighagen
By reporting openly on problems we find in the melting point datasets I think we can soon provide a highly curated open collection for anyone to use for experimental or modeling purposes. If anyone knows of other open datasets please contribute them. - Jean-Claude Bradley
Speaking of my previous comment, Andy has pooled together the data we have curated to date and included CDK descriptors which should be helpful for open modeling - total 12634 measurements - see ONSMP013 - Jean-Claude Bradley
"we can soon provide a highly curated open collection for anyone to use for experimental or modeling purposes" -> very important indeed! #cc0 again? You're getting things done here that others in the BO unmovement have not been able to do wrt getting chemistry data out in the open... well done! - Egon Willighagen
Bill, I think melting point is a problematic value because the purity of the sustance affects the final result. In the movie Blow, there's a scene where the dealer measures the melting point - the higher the number the higher purity of the drug. - Elizabeth Brown
There's a more fun way to check how good the coke is... - Bill Hooker
well, the dealer tests it after that in the next scene, just to make sure... - Elizabeth Brown
@Bill, not an expert in blow but assuming you mean magic angle spinning NMR. I had a chemist friend from Queens explain MAS to me once. A _chemist_ ... _Queens_... coincidence??? - Steve Koch
Elizabeth - yes impurities will lower the melting point. If students record melting points in my lab they will also take an NMR to demonstrate the purity. But I don't think that would not account for these extremely large differences we're finding. - Jean-Claude Bradley
Jean-Claude Bradley
Alfa Aesar melting point data now openly available -
Alfa Aesar melting point data now openly available
This amounts to a collection of currently 13,436 Open Data melting point values. We believe that this is currently the largest such collection and that it should facilitate the development of completely transparent and free models for the prediction of melting points. - Jean-Claude Bradley
Congrats! Left a comment in the blog, asking for clear copyright/license statements, which I could not find so far... - Egon Willighagen
Egon - sure we'll put a CC0 logo as we do with the solubility data pages like this - Jean-Claude Bradley
Jean-Claude Bradley
The Spectral Game with ChemDoodle -
The Spectral Game with ChemDoodle
Through a collaborative effort between Kevin Theisen, Andrew Lang, Antony Williams and myself, we now have a non-Java based version of the Spectral Game at - Jean-Claude Bradley
Cameron Neylon
Can a journal make a difference? Let’s find out. -
I didn't realize U Cambridge had shifted to Sweden :) - Rajarshi Guha
No, its just the Egon is moving so fast at the moment that he takes places with him...will get that corrected. Egon, what is the best affiliation? - Cameron Neylon
I notice that structures can be deposited with PubChem "Chemical structures and assays Structures of chemical substances can be deposited with PubChem Substance." WOuld you be willing at also add in ChemSPider as a place to deposit structures? - Antony Williams
On "In the way it conducts peer review, ... [it] will be a very ordinary journal." - what about public peer review, or at least posting the reviews? - Daniel Mietchen
Posting the reviews would definitely enhance clarity around what are considered applicable best practices. - Heather Piwowar
Yep, the intention is to post the reviews. Though the usual caveats on this apply. It's harder to do than it looks. What I'd really like to do is version the papers of course... - Cameron Neylon
Benjamin Good
I just read this: "The journal RNA Biology, in collaboration with Rfam, has pioneered a new model of scientific publication where scientists are required to write a Wikipedia article to go alongside their manuscript paper" - has anyone heard how this working out?
From the instructions to authors "Publication in the track will require a short manuscript, a high quality Stockholm alignment and at least one Wikipedia article; each centered around the RNA in question." - Benjamin Good
Isn't that agreement two years old? It works quite well - RFAM team has recently published paper on this model (cannot find it now). - Pawel Szczesny from iPhone
not sure, just came across it for the first time today - Benjamin Good
Original paper announcing RNA Wiki Project - and that recent paper discussing among others pros and cons using Wikipedia: - Pawel Szczesny
Thanks for the refs! Looks like their experience was very similar to the Gene Wiki project. - Benjamin Good from email
We get a steady trickle of publications. I still need to solicit from the community quite a lot. For example, I recently sent a lot of invites out for miRNA family reviews. I'm hoping one day the track will snowball along the lines of the NAR special issues. In addition to the above links, I discuss this further here: - Paul Gardner
I would really like to see some #OA journals go that route. So far, however, their interest to do so (if any) is not very visible. - Daniel Mietchen
I'm not sure it would always be clear what WP articles should be written or updated WRT any given body of work. I could certainly see encouraging adding references & text where applicable to existing WP articles. This would need to wait until after publication and couldn't form part of the review process. For review articles it would be easier. - Paul Gardner
I think the keywords would provide a good first guess on what articles to update or start. - Daniel Mietchen
Worth a try. Get Phil Bourne on the phone. - Paul Gardner
Bill Hooker
Wikimedia Blog : WissensWert – Wir investieren in eure Ideen! -
"Wikimedia Deutschland wagt heute ein Experiment: Wir investieren in mutige Ideen zur Förderung Freien Wissens und stellen ausgewählten Initiativen kurzfristig und unbürokratisch Mittel in Höhe von 500 € bis zu 5.000 € zur Verfügung." - Bill Hooker from Bookmarklet
English: today, Wikimedia Germany dares an experiment: we will invest in bold ideas to advance Free Knowledge and provide selected initiatives with short-term, unbureaucratic means from 500 to 5,000 Euros to achieve their goals. (corrections to my translation welcome!) - Bill Hooker
Seems to me someone in this community might have a project in mind that would fit that price range... - Bill Hooker
your translation is perfect. - Martin Fenner
Submissions only in German (but we can crowdsource translation here); "advance Free Knowledge" is being broadly interpreted, some considerations are: sustainability, how well the project can continue after the funds are spent; generalizability, how well it translates to other areas and endeavours and also whether it solves an important general problem that stands in the way of Free... more... - Bill Hooker
What about a project that systematically reviews certain kinds of Open notebooks, data, code, papers etc., with funds available as prize money for the best reviews and best reviewed items? - Daniel Mietchen
I inquired whether would fit, and they replied that they see no formal criteria that would exclude it. Now thinking of combining it with as two approaches to a Library of Open Science (as per ). - Daniel Mietchen
I wonder whether the idea of (once the articles are formated into wiki) translating into relevant languages (e.g., chagas articles into spanish) to have the content incorporated in #olpc deployments (or similar) would be something that might be added to the proposal. - Kubke
Converting OA articles into wiki entries is one thing, translating scholarly content into something useful for olpc use quite another. And while the former can be automated to a large extent, the latter can only partly, at best. Certainly too early this time. - Daniel Mietchen
Thanks Daniel. But yes, getting the initial part (conversion into wiki) would be the necessary first step for the latter. Let me know if I can be of any help. - Kubke
Our draft is at . Deadline tomorrow. - Daniel Mietchen
Looks good to me! - Björn Brembs
Translation & final phrasing now in process at (please ignore formatting - the entries to each point will finally have to be pasted into the submission form anyway). Help welcome. - Daniel Mietchen
Submitted. Will try to reformat later and to translate the final phrasings back into English. Help appreciated. - Daniel Mietchen
Fixed formatting and transferred the German version to the wiki: . English version nascent at – help with translation appreciated. Anyone have an idea for illustrations? - Daniel Mietchen
Illustrations? Not sure I understand what for - Kubke
Why illustrations? The page will be subjected to public review by anyone interested, so improving the presentation of the content is probably a good idea. The popular vote will be taken into account when making the funding decisions. Any other suggestions on how to improve presentation are also welcome. - Daniel Mietchen
Oh, I see: (1) 'dead paper brick wall' with the plant growing on top: (2) Consumable open access (3) Caged (4) I like this key because it makes me think of the two 'P's' of panton principles - Kubke
I like this cause it needs no explanation - Kubke
These are good ones indeed, Kubke - thanks! - Daniel Mietchen
I have a photograph at home of a toilet paper roll feeding into a typewriter with the opening text of Don Quijote de la Mancha - Kubke
Sounds like copyrighted, though a good fit otherwise. Anyway, the current version has the paper brick image and the phrase "Paper provides multiple options for reuse", which will probably (especially in the German version) ring the toilet paper bell but more subtly. Looking into ways of getting the key and the cake in. - Daniel Mietchen
Oh, it is times like this I wish I knew german :) The cake for me elicited the ability to consume the content. (and dare I say, recycle it!) The caged girl with the butterfly is the image I have of the current state: Locked-in creative process with barriers for interaction. The key one would think could really go anywhere where the concept of unlocking is brought up. - Kubke
You may probably need to add the licencing to the images (since they are not CC0) and do the attribution (I think they all have BY in the licence) - Kubke
Yes - I am used to do this via templates but haven't set those up on this wiki yet. License is indicated at the individual page of each image, though. - Daniel Mietchen
Done translating into . Anyone willing to proofread? Will deal with the images later. - Daniel Mietchen
I read the English version (sorry, too slow in German, would take me days!) and cannot find any place for improvement in the language. One suggestion: although the science3.0 community is the team, there are clearly some key personnel here. I think it might strengthen the application to name them and make explicit their deep connections to the target community. - Bill Hooker
Thanks for the comment, Bill - the submission was on Oct 15 (via a form, with character limits), and in the interest of fairness, I think we should stick to the submitted text even in the translation. Official release of the (valid) submissions now scheduled for Monday. - Daniel Mietchen
40 projects have been considered eligible: , including ours at (Science as a wiki, #89 - English version available via... more... - Daniel Mietchen
I voted for Wissenschaft als Wiki, the festival, the translation into kiswahili, the CC promotional materials one and, um, I forget the last one I voted for. - Bill Hooker
Just voted for Wissenschaft als Wiki, Wheelmap, WikiStories, Open Hardware and Design Alliance, - . Voting ends tomorrow (Nov 30). - Daniel Mietchen
Eight winners have been announced today: . Ours is not amongst them. - Daniel Mietchen
:-( - Bill Hooker
Oh bugger! - Kubke
How much money was this for? Internet NZ has a set of $ for projects. Since it is written (and translated) would you consider trying that? - Kubke
Damn. Well done anyway Daniel, it was an amazing effort. - science3point0
@Kubke - this one was for 5k Euros max (we had requested 3213, mostly for developer tasks and server hosting). Can you give more info on the Internet NZ option? In any case, the proposal is ready for reuse. - Daniel Mietchen
@Daniel The funding info is here I think the application would need to be rehash a little its importance/potential impact for the Pacific (at least mention as an example). This should be relatively easy, considering that much of the science would have significant health and educational impacts, and by being in a wiki format that can be updated... more... - Kubke
Had a look at their conditions now. "Grant applications must: * support outcome/s that meet at least one of the Objects of the Society;", which are ( ) " * To promote easily available access to the Internet for New Zealanders including fibre to every home. * To develop, maintain and disseminate standards for the Internet and its associated technologies... more... - Daniel Mietchen
Yes, I could talk to the catalyst people, and I could also try to get a hold of a couple of people at internetnz who could tell us right away whether we should bother or not. Didnt want to do it until there was some consensus. As for catalyst, yes I do know some people there, but to clarify, it is (as far as I know) not an NGO, but an actual for profit business which happens to be built around OSS. I'll ask around, and if not, KiwiFoo is in mid-February, so I could propose a session and see what happens. - Kubke
OK, feedback I got is that InternetNZ is probably not the best place to go to. But will bring this up at kiwifoo and see what options may come out of there. - Kubke
Next try is up: - deadline for expressions of interest is in 20min. Mine has already been submitted, and the final submission will have to be posted at by Oct 28 German time. - Daniel Mietchen
Bill Hooker
Limitless or limited resources. | Indexed -
Limitless or limited resources. | Indexed
Thought experiment: Replace "ideas" by some other noun. I just tried "XML", "money", "weapon-grade Plutonium", "jokes" and "problems", and they all still fit into this general depiction. - Daniel Mietchen
Carl Boettiger
How do you manage citations when writing on the web (blogs, etc?) Would be nice to have a reference manger that works in browser editors like #Mendeley does in office docs
It would be really nice if the Google Docs API supported the right hooks for use to do this. - Mr. Gunn
When you say manage, do you mean insert during the writing process? - AJCann
Yup, that would probably be the most valuable. For instance, even a Wordpress plugin that let me cite using the bibtex reference would be quite nice, if such a thing exists? - Carl Boettiger
Good news: bibtex wordpress plugin exists. bad news: formatting fails on my site. - Carl Boettiger
Got a basic citation system working in wordpress at least: - Carl Boettiger
My thoughts on this are here: Briefly, we should integrate citations as Wordpress links, this would give us a lot of interesting features for free. - Martin Fenner
Thanks Martin, that's an excellent piece. Yes, I agree citations should be put in as links, though I'm not sure what links: as @rmpage points out, doi based links might make more sense than those pointing to a particular publisher? What track-back tools are available that could determine how many incoming links a paper has? How do these cope with multiple potential link urls to the same paper? - Carl Boettiger
Carl, you point a big problem that goes beyond managing citations for a blog. I'm a big fan of DOIs, and I'm always confused why so many places prefer their own internal identifier (PubMed is a prime example). - Martin Fenner
Bill Hooker
Future Internet | Free Full-Text | Simplifying the Scientific Writing and Review Process with SciFlow -
"Abstract: Scientific writing is an essential part of a student’s and researcher’s everyday life. In this paper we investigate the particularities of scientific writing and explore the features and limitations of existing tools for scientific writing. Deriving from this analysis and an online survey of the scientific writing processes of students and researchers at the University of Paderborn, we identify key principles to simplify scientific writing and reviewing. Finally, we introduce a novel approach to support scientific writing with a tool called SciFlow that builds on these principles and state of the art technologies like cloud computing." - Bill Hooker from Bookmarklet
Björn Brembs
gg » What has changed in science and what must change. -
"First of all, I think it is worth noticing that this is an extremely hot topic, yet not really controversial among scientists. No matter whom you talk to, not only does everyone agree that the status quo is completely inadequate but there also seem to be a consensus on what kind of things need to be done and how. In particular, everyone agrees that 1. more funding is needed 2. the current ways of distributing funding and measuring performance are less than optimal" - Björn Brembs from Bookmarklet
Sounds like the start of an interesting discussion. The need to separate good teachers from good researchers really resonates with me. Other parts, I have mixed feelings on. - Chris Miller
It's nice to see the favourite topics of our little FF echo chamber popping up independently in so many different places. - Bill Hooker
"You cannot expect unproductive tenure holders to give up their job [...] These are problem that only funding agencies can solve [...]". Good thing those "unproductive tenure holders" aren't on the funding agencies' grant panels... - Eric Jain
Mr. Gunn
Can just do SOME of them? Maybe IRT @nicolibrarian: Do's and Don'ts of taking care of baby:
Can just do SOME of them? Maybe IRT @nicolibrarian: Do's and Don'ts of taking care of baby:
Yeah, you're thinking of the dryer, not? :) - Egon Willighagen
(Oh, and of course, that lady in the right-bottom most advice has a suspicious number of baby deaths during her career... you saying...) - Egon Willighagen
it does say it's about babies. all I can say as the father of twin boys that containing them has numerous options...and they actually anjoy them! - Antony Williams
we've thought about the hosing down one a few times... - Elizabeth Brown've only thought about hosing them....those hot summer days in NCare a perfect excuse for hosing... - Antony Williams
as an infant, no. After that there was lots of hosing.... - Elizabeth Brown
Rafael Sidi
in dayton with the SciVerse team, preparing for the SciVerse Application beta launch, exciting stuff
Grand Effect
Let’s Cut the Hype: Facebook’s Email Service Won’t be a “Gmail Killer” (a little Friday night rant...)
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