Egon Willighagen - Discussion

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Egon Willighagen shared an item on Google Reader

CDK-Taverna Version 0.5.1 released

Thursday at 2:01 pm - Link

Cameron Neylon, Deepak, Rajarshi Guha and Dan Gezelter liked this

Thomas has been uploading workflows to myExperiment.org, so learning CDK-Taverna is becoming easier and easier... - Egon Willighagen

Pierre posted an entry on Connotea: lindenb's bookmarks

cexcept - exception handling for C

14 hours ago - Link

Programming languages are converging more and more... - Egon Willighagen

Cheminformatics: Egon Willighagen posted a link

“Does anyone know a site which does a good, and more detailed, review of "R" packages? i.e. say what they are used for? (R as in http://www.r-project.org/)”

12 hours ago - via Reshare - Link

On R documentation... - Egon Willighagen

Jean-Claude Bradley posted a slide show on SlideShare

Manchester Open Notebook Science Talk

Friday at 10:11 am - Link

Egon Willighagen, Cameron Neylon, Graham Steel, Duncan Hull and 3 other people liked this

Thanks again for coming, looking forward to more collaboration in the future. Did you get to Edinburgh OK? - Duncan Hull

Egon Willighagen shared an item on Google Reader

Looking for Assistance with Carbohydrates (ChemSpider Blog)

yesterday at 12:07 am - Link

A bit too far from organic chemistry right now; and don't know anyone from PRI who works with plant sugars either... - Egon Willighagen

Pawel Szczesny posted a message on Twitter

“I need serious knowledge management system. It's ridicolous to open 4-5 applications just to have an overview what needs to (or can) be done”

Friday at 12:50 pm - Link

Hutch Carpenter, Fitzgerald Steele and Cameron Neylon liked this

Do you mean how to get things done? A NextAction list and a Project list do it for me: have always a pretty good idea on what needs to (or can) be done. One filofax does the trick... - Jan Aerts

Not really. Here's example: I get draft of a paper/project (Word), and some alignments (Jalview), I have my own notes (Freemind) and looking at first raw results (Firefox). All these span across two or three monitors, since I'm trying to connect some dots and wrap my head around the project, so I want to see everything at once. I don't mind dozens of windows - but data presented in each cannot be linked (I cannot click on the A43H mutation in the Word and have it highlighted in Jalview). - Pawel Szczesny

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I'd love to have a single application I could throw in and manage all bits and pieces. Closest example I've seen so far was ICM Browser Pro - application where you can visualize protein structure and annotate it (next to the 3D view window) with wiki-like text, where links can point to particular view/representation. - Pawel Szczesny

Have you tried Evernote? That might work by organising stuff by project - Sally Church

Thanks Sally. Yes I have tried, and while I like OneNote little more (especially searching for text within images), both are great when only text is involved. That's actually my replacement for Freemind when the project is not yet structured very well. However, when data comes into play, it's not that useful. And writing data handling plugins isn't probably very straightforward in both cases. - Pawel Szczesny

I think Yojimbo does something like this on the mac, but I am constantly in search for the same as well (which reminds me I need to try Yojimbo and see if it matches the hype) - Deepak

Deepak, you may be satisfied with Journler - it has much more impressive feature list (I was using it when I had a mac; it was wining hands down over Yojimbo at that time). - Pawel Szczesny

Argh ... another new thing to try :) - Deepak

I'm still looking for a good tool like Getting-THing-Done (or the NextAction/Projects lists) allowing me to put items in perspective (Home/Work/...) which works both online and offline... the latter is important to me too... I've been thinking about hacking something up using Git, but the GUI is time consuming, so rather use something existing... (and yes, a A5 booklet works well, expect that it does not integrate the organization of my TODOs) - Egon Willighagen

Deepak, I have the same situation ;) BTW, Egon just pointed Neil to Bioclipse and I think it's another example of such system made for biosciences. I haven't looked at it for some time, but it's actively developed and worth to try ( :D ) as well. - Pawel Szczesny

Bioclipse I have :) - Deepak

Egon, you may try (I will smile the whole day of that) Toodledo - it's mostly online, but it has an exporter to a printed booklet (printer not included). The nice thing about it is that incorporates long term goals - that's pretty unique among GTD software. - Pawel Szczesny

I use OmniFocus for stuff that needs to get done, and then throw everything else (links, PDFs, result data, code snippets, web pages etc) in to Yojimbo. Folders, tagging and smart folders take care of organising things. Can definitely recommend it. - Matt Wood

Egon Willighagen shared an item on Google Reader

Dustin Kirkland: Announcing the Ubuntu Manpage Repository: manpages.ubuntu.com

Friday at 11:05 pm - Link

Andrew Perry liked this

Nice to have a trustworthy manpage facility. Oh, and more of me on the net: http://manpages.ubuntu.com/man... :) Open [Data|Source|Science|...] is so rewarding, that it is addictive... Is that why it works? - Egon Willighagen

Neil Saunders posted a message on Twitter

“finally getting head around eclipse; like ide concept but does eat resources”

Friday at 10:34 pm - Link

Pierre, Cameron Neylon, Egon Willighagen and Deepak liked this

Make sure to check out http://www.Bioclipse.net... - Egon Willighagen

Eclipse for perl ? Or will you have a glance at java ? - Pierre

right now, playing with ruby/rails - Neil Saunders

Egon Willighagen posted a message

“I wish MyExperiment.org had a RSS feed for my activities there to share here on FF...”

Thursday at 1:20 pm - Link

Deepak, Duncan Hull, Cameron Neylon, Pawel Szczesny and 2 other people liked this

I wish all research activity had an RSS feed for that reason - Neil Saunders

+1 for Neil. Everything should have a nice rich faceted feed. You can do so much cool stuff with it. - Cameron Neylon

If you really want this then email it myexperiment-discuss@nongnu.org - Duncan Hull

coordinated strike guys? - Cameron Neylon

Or http://www.myexperiment.org/fe...; Just send a message there... - Egon Willighagen

PauloNuin posted a link

This Post Not Made In Chrome; Google's EULA Sucks

Wednesday at 7:09 am - Link

Björn Brembs, Sally Church, Cameron Neylon, Michael Kuhn and Michael Barton liked this

Why would Google add that text to the EULA? Surely they must have that it would have been quickly found and posted all over the web. They'll just end up removing it anyway. - Michael Barton

Yep. Just had an email from IT here at Sanger that we're not allowed to use Chrome either. Because of that clause in the EULA. - Jan Aerts

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I'm usually a fan of Google, but this just seems crazy. I don't buy in for all the hyperbole that you see on Slashdot etc, but I agree with whoever wrote that you might expect this from MS but not from Google. - Michael Barton

This is in the standard Google TOS, so it also applies to GMail if you view it that broadly - Michael Kuhn

There is something similar I think in the Google Research Data EULA but there you only have the choice of Public Domain or CC-BY anyway so it hardly matters - Cameron Neylon

Ars Technica: "Google on Chrome EULA controversy: our bad, we'll change it" http://arstechnica.com/news.ar... - Michael Kuhn

http://googleblog.blogspot.com... - Thomas Lemberger

That was a fast response. - Michael Barton

The almighty blogosphere strikes again? - Cameron Neylon

With Open Source, all bugs are shallow :) - Egon Willighagen

Neil Saunders posted a message on Twitter

“ok, we *really* need something to handle duplicate shared items at FF now; especially in the communities I frequent”

Thursday at 9:38 pm - Link

Voyagerfan5761, Roland Krause, Richard Akerman, Matt Wood and 4 other people liked this

Its a feature not a bug. A bit like buggotea no? http://www.nodalpoint.org/2006... I don't think you'd ever be able to eradicate it completely. Discuss. - Duncan Hull

It is a feature. I'd like to see one or both of: (1) a message along the lines of "also shared by A, B, C and X other people"; (2) ability to reshare a posted item to my account at the same service without my reshare then appearing as a FF share. - Neil Saunders

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Duplication is not really the problem, IMHO, but the fragmentation is. I'd too like to see 'also shared by' or 'also shared here and there', or a 'see other shares for this link'. - Egon Willighagen

I would like to see 'also shared as' with a link to the other items - Cameron Neylon

I'd like to see an option "consolidate reshared items" - otherwise I see the same posting multi-times, as it makes its way into the various science rooms. - Richard Akerman

Reshared to FriendFeed Feedback, with apologies for reshare :) - Neil Saunders

When you reshare, the word "Reshare" is a link to the original item. If comments would travel with reshared items, that would avoid fragmentation (though you'd get more duplication, of comments this time). I'd be happy with that. - Bill Hooker

In other words we want true comment and item federation withing the friendfeed namespace :) - Deepak

Egon Willighagen bookmarked a page on delicious

Molecule Kernels: A Descriptor- and Alignment-Free Quantitative Structure–Activity Relationship Approach

Thursday at 2:12 pm - Link

An old idea really, but interesting to see how they define alignment-free similarity... the abstract does not say, and I don't have access until I arrive in Uppsala... - Egon Willighagen

Well the method of Ballester and Graham Richards allows for 3D similarity measurement without alignment. Alternatively, pharmacophore derived descriptors could be alignment free (depending on the nature of the groups) I haven't looked at it yet, but 'descriptor free' ?? I'm curious - a model without input features? - Rajarshi Guha

Egon Willighagen bookmarked a page on delicious

Searchme Visual Search - Beta - rev. 2.0.2

Thursday at 2:09 pm - Link

Visual index to my web presence... - Egon Willighagen

Egon Willighagen shared an item on Google Reader

myexperiment.org plug-in for Taverna

Thursday at 2:01 pm - Link

Cameron Neylon, Jean-Claude Bradley, Deepak and Rajarshi Guha liked this

I've read about this MyExperiment plugin for Taverna, but had not seen the inline list with previews... really nice indeed! - Egon Willighagen

Cameron Neylon posted an entry on Science in the open

The Open Science Endurance Event - Team JC-C

Thursday at 12:55 pm - Link

Graham Steel, Michael Barton, Pawel Szczesny, Jean-Claude Bradley and 2 other people liked this

Will be going to Jean Claude's talk in a couple of hours - Michael Barton

Cool - I meant to email because I wasn't sure you would know about it - Cameron Neylon

JCB did a great talk here in Manchester, lots of interesting discussion afterwards. Thanks Cameron for organising it and thanks JCB for doing it! - Duncan Hull

Good talk. Usual questions, IP and scooping. - Michael Barton

It went well and we had a good discussion - I'm uploading the talk on Google Video right now.... - Jean-Claude Bradley

Cameron Neylon posted an entry on Sortase Cloning - blogs@ChemTools

Comment: Re: Weighing of dried samples

Thursday at 12:53 pm - Link

Egon Willighagen liked this

Egon Willighagen bookmarked a page on delicious

MeltDB: A software platform for the analysis and i...[Bioinformatics. 2008] - PubMed Result

Thursday at 11:28 am - Link

http://meltdb.cebitec.uni-biel... - Egon Willighagen

The Life Scientists: dekay posted a link

“Does anyone know a site which does a good, and more detailed, review of "R" packages? i.e. say what they are used for? (R as in http://www.r-project.org/)”

Thursday at 4:18 am - via Reshare - Link

Pawel Szczesny, Chris Miller, Neil Saunders and Pierre liked this

R News? - Egon Willighagen

There's an R wiki; http://wiki.r-project.org/rwik...; don't know how comprehensive - Neil Saunders

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Documentation/examples is not a strong point of R, it must be said - Neil Saunders

R views might be what you're looking for: http://cran.at.r-project.org/w... - Michael Barton

This page is pretty good too: http://www.nettakeaway.com/tp/... - Michael Barton

Did you have a look at the views http://cran.r-project.org/web/... ? They contain a list of packages to be installed as well as a short description of what you can do, although those are rather task oriented. Otherwise the RSeek search engine (http://www.rseek.org/) has become my favorite source of information. - Yann Abraham

@all: thank you for your links: here is my summary: http://www.twine.com/item/11fz... - dekay

Visualization packages: http://addictedtor.free.fr/gra... - dekay

Cameron Neylon posted an entry on Sortase Cloning - blogs@ChemTools

Comment: Re: Weighing of dried samples

Thursday at 2:49 am - Link

Jean-Claude Bradley and Egon Willighagen liked this

Cameron, good to see you are measuring knowns too... good for determining person, method, site, day, etc bias. - Egon Willighagen

Absolutely - and now with any luck we will have a bunch of people measuring the same things via different methods - Cameron Neylon

Interesting that this came through on my feed actually given the comment was written by Jenny and not me. Will have to check up on that. - Cameron Neylon

Cameron Neylon published photos on Flickr

Wednesday at 8:15 am - Link

Aarthy, Mr. Gunn, Jean-Claude Bradley, Egon Willighagen and Rajarshi Guha liked this

Pierre posted a message on Twitter

“I just wrote my first Ubiquity Script: ! Achoo ! Wee Woo !! http://tinyurl.com/6l2f3f”

Tuesday at 1:21 pm - Link

arnet and Egon Willighagen liked this

Egon Willighagen posted a link

Stephen Fry on Open Source, citing the openness of Science...

Tuesday at 12:17 pm - Link

Graham Steel and Eva liked this

I saw that yesterday (and noticed his reference to science) but was too lazy to post the link. There's also a video on VideoJug where Fry talks about science and how it should be open. - Eva

Eva, what's the link for that? - Egon Willighagen

Egon Willighagen shared an item on Google Reader

Creating and Reviewing Patches in the Chemistry Development Kit (CDK)

Tuesday at 12:17 pm - Link

Rajarshi Guha liked this

And slowly we are moving towards a healthy multithreaded development eco system. Open of course. - Egon Willighagen

Applying the patch... with the regular merging horror... I would I love to see git do this for me... it seems possible: http://www.jukie.net/~bart/blo... - Egon Willighagen

Pierre posted a message on Twitter

“OK, I'm installing mozilla ubiquity”

Tuesday at 12:06 pm - Link

Ha, you can't resist either? :) It costed me most of Sunday night... - Egon Willighagen

and still, this is crude, much more than Quicksilver ever was. we need this on OS level. - dekay

The Life Scientists: Martin Fenner posted a link

Elsevier Article 2.0 contest rules posted

September 1 at 11:30 pm - Link

Andrew Perry, Sutee Dee, Jason Winget, Egon Willighagen and Deepak liked this

By entering the Contest, participants grant Sponsor and its affiliates, the rights, without limitation or further permission or compensation, to: (i) use and publish their name, likeness; and (ii) use, create, reproduce, modify, publish, display and distribute their Applications. - Martin Fenner

The submitted Applications must not be, in whole or in part, governed by any license that requires, as a condition of use, modification, or distribution of software, that such software or other software combined or distributed with such software be: (i) disclosed or distributed in source code form, (ii) licensed for the purpose of making derivative works, or (iii) redistributable at no charge. - Martin Fenner

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So, what they want is people working for them for free to do fix their broken publishing model, and be the sole owner of that outcome? Fair, I guess :) hahahahaha - Egon Willighagen

Although I clicked "like", that's not really how I feel. They more or less just ensured I won't enter. Not only would I want anything I managed to write to be open-source, many of the tools I had planned on using make this a *requirement* - Jason Winget

Jason, I hit *like* because I like the discussion about the link... there is some ambiguity in the meaning indeed. I actually will not join with this requirements, and really disappointed about them. - Egon Willighagen

Looks like Elsevier wants to create some buzz, but they come out looking cheap. I can understand their requirement that the submitted code must not have special licensing terms. But $4K for the main prize? Competing for the $1M Netflix Prize (which moreover only requires you to sign a "non-exclusive grant of license") seems like a better (and fairer) deal to me. But maybe some starving postdocs will bite :-) - Eric Jain

After reading the rules I will think again about participating in the contest. But the most interesting aspect of Article 2.0 is not the software, but rather the concepts of how a paper is presented online. This could ignite an interesting discussion for our benefit. - Martin Fenner

It sounds like the rules say no GPL code, but Apache-style licensing might be okay ? (It's not 100 % clear to me, I'm no license lawyer. The sample code is under the Apache license. Maybe Rafael Sidi knows ?). I agreed to be a Contest judge, so I'm not allowed to enter :) (and I guess I should remain tight lipped about my ideas so as not influence the entries). It will be interesting to see what people come up with ... I hope the licensing requirements don't limit the quality of the entries too much. - Andrew Perry

Neil Saunders posted a message on Twitter

“back from LIMS meeting; "our paper notebooks are more convenient", they say and I do believe them, but that's not the point”

September 1 at 7:08 pm - Link

dekay and Egon Willighagen liked this

Shakes head - Deepak

At the moment, you can't just pick up a laptop from wherever someone left it laying on the bench and start writing/drawing. Until laptops.tablets become as commoditized as pencils and paper, I don't know if anything will change. - Mr. Gunn

As I say in the related blog post, I understand absolutely why pencil and paper are the preferred tools in the lab. Resistance to any form of electronic project management - less understanding :) - Neil Saunders

At 'sciblog' there was a comment on cleaning up LN entries, like missing data, narrative etc... this might be the right moment to digitize the entry, instead of digitizing it at the bench. For example, one would write up details before the experiment, write the comments during the experiment on paper, and add them to the electronic record later... Point, it's not a black and white world. - Egon Willighagen

There is a project at work where we are trying to figure out how an electronic LN needs to look like -- getting most of our 200+ labs on board. Thinking KISS here, as in "print to pdf" ;) - dekay

The Life Scientists: Thomas Lemberger posted a link

PubMed search in Ubiquity

September 2 at 12:18 am - Link

laura, Rajarshi Guha, PauloNuin, Deepak and 12 other people liked this

I am not a programmer and have zero idea about Javascript, so had many problems. Improvements most welcome! Couldn't use properly the xml from ncbi's E-utilities (wrong mime-type???) :-( Anyway, to use the command, copy-paste the code into Ubiquity's command-editor (read more: <http://is.gd/1Wns>). Try a PubMed search by selecting something on the screen, call Ubiquity (option-space) and type 'pubmed', wait and see... - Thomas Lemberger

nice examples on the Ubiquity homepage - Pedro Beltrao

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Brilliant, I love it.. Didn't seem to save the command when I restarted the browser though - Jason Winget

added a little feature to select number of records displayed (eg include #3 somewhere in the query to limit to 3 records) and moved the code to http://code.google.com/p/tl-ub... - Thomas Lemberger

For parsing XML, jQuery is very nice and it's included in Ubiquity. No need to do match() :) - Rajarshi Guha

mmh, I tried this but it did not work... unfortunately ncbi's e-utils return text/html but jQuery expects text/xml (<http://is.gd/bu6>). Is there a workaround? - Thomas Lemberger

if retmode is xml, I can work with it in jQuery. Also in jQuery.ajax() you should set the type as xml. Also, namespaces need to be separated from the element by ':\\'. See http://groups.google.com/group... - Rajarshi Guha

I have a PubMed/JSON proxy in Scintilla if you need it - would make this much easier. - hubfeed

var parser = new window.DOMParser() - Thomas Lemberger

Egon Willighagen bookmarked a page on delicious

http://wwmm.ch.cam.ac.uk/maven2/uk/ac/cam/spectra/spectra-cif/0.2-SNAPSHOT/spectra-cif-0.2-20070402.110419-1.pom

September 1 at 6:21 am - Link

CDK should autogenerate .pom files. - Egon Willighagen

Science Blogging 2008: Maxine posted a link

London's dead. The party's over. - Mixed miscellanies - Scott Keir's blog on Nature Network

August 31 at 1:23 pm - via Bookmarklet - Link

;-) - Maxine via Bookmarklet

Yeah, sorry about that... we went to Cambridge: http://blog.openwetware.org/sc... - Egon Willighagen

Science Blogging 2008: Egon Willighagen posted a link

Guys (and Grrls), as requested in the afternoon unconference in the library: use ubiquity to add semantics while blogging -> "Ubiquity fun: entering semantic...

August 31 at 7:51 pm - Link

Lisa, Richard Akerman, Pierre and Neil Saunders liked this

Might anyone test this on Nature Network, please? - Egon Willighagen

From what I see in the screenshots, it probably won't work on Nature Network. NN adds links in a different way. Not html but with quotation mark. A link there would "look like this":http://### - Eva

Egon, thanks for your scripts and for pointing me to ubiquity. Your resolve-doi script seems to require a rich text editing field. Nature Network (and probably many other blogs) uses Textile and complains. - Martin Fenner

Egon, the add-doi and sechemtic-inchi scripts work in a Nature Network blog editing field. But again, the output is HTMl and not Textile. But this requires only minor tweaks and is a great way to put together a set of science blogging tools. - Martin Fenner