Egon Willighagen › Comments

There is also a Balloon plugin for Bioclipse. - Egon Willighagen

I would... first thing I do when people report that the CDK has a bug is to validate what they input. At least in 20% of the time (very conservative estimate) it is bad input. - Egon Willighagen

Rajarshi was written a convenient helper program using the CDK to create a PDF from a SD file: Batch generation of 2D diagrams After downloading the draw2d.jar, you can do: java -jar draw2d.jar your.sdf It has several command line options to tune the output: usage: draw2d [OPTIONS] sdf_file Draws 2D images from coordinate files. Default output is PNG and input should be an SDF file. -c,--scale Scale factor (default is 0.9) -f,--format Output format (PNG, JPEG, PDF) -h,--help Give this help page -l,--color Color atoms -n,--ncol How many molecule columns should tabular output have. The number must be 1 or more -o,--outputDir Where to dump images (default is current directory) -p,--props If present output properties in the PDF table. Default is no -s,--showH Show explicit hydrogens (default is no) -t,--table Output structures as a tabular PDF. This option overrides the format option and the output file is called output.pdf -v,--verbose Verbose output -x,--x Width of the images (default... - Egon Willighagen

The software is GPL-ed licensed :) - Egon Willighagen

Set of nice cheminformatics questions... - Egon Willighagen

A comprehensive update on the human protein resource - Frank from iPhone

Egon, It was just made with the titles of the articles. Anyway, the word "RDF" doesn't appear in the abstracts - Pierre Lindenbaum

It's amazing how some US citizens can be so blind to not see where market economy fails... free market requires buyers to be able to decide, "no, perhaps when you lower your price..." But it just does not work like that for health care... or housing... there does not exist something like a free market when basic needs are involved... - Egon Willighagen

@Benjamin -- we're working on it. I should have said "temporarily" or similar. Can't explain in detail -- public company disclosure blah blah blah. Suffice to say I'm not being exploited, and didn't want to give that impression! - Bill Hooker

Perhaps graphically summarize the full details...? Time line of papers per year...? - Egon Willighagen

Interesting thought Egon ...are you aware whether there is anything in their API to allow us to retrieve this type of information? - Antony Williams

EUtils lets you get counts of articles within a time period - Rajarshi Guha

The CDK used to have a library to validate chemical graphs against common problems, including unknown atom types. Additionally, the file reader for the MDL SD format has a STRICT mode, which makes it fail if the file is not conform the format. However, the CDK currently does not have a library of command line utilities that make functionality available. What Open Source tools are available to inspect the file and the content of a MDL SD file, and report errors? - Egon Willighagen

it would surely be just an estimate, but the error because of the data set may not be higher than the general error on impact factors... (which is an interesting question in itself...) - Egon Willighagen

@Mr Gunn... yes, such an API would be perfect. I'd like to hear more about that... - Egon Willighagen

the exam was based on the following source: http://getcheminfo.wikispaces.com/FAQ - Jean-Claude Bradley

and actually that question about ACS self-archiving came directly from a FriendFeed conversation with the kind help of Graham and Dorothea :) http://ff.im/buFyT - Jean-Claude Bradley

BMC Bioinformatics, Vol. 10, No. 1. (3 December 2009), 397. BACKGROUND:Contemporary biological research integrates neighboring scientific domains to answer complex questions in fields such as systems biology and drug discovery. This calls for tools that are intuitive to use, yet flexible to adapt to new tasks.RESULTS:Bioclipse is a free, open source workbench with advanced features for the life sciences. Version 2.0 constitutes a complete rewrite of Bioclipse, and delivers a stable, scalable integration platform for developers and an intuitive workbench for end users. All functionality is available both from the graphical user interface and from a built-in novel domain-specific language, supporting the scientist in interdisciplinary research and reproducible analyses through advanced visualization of the inputs and the results. New components for Bioclipse 2 include a rewritten editor for chemical structures, a table for multiple molecules that supports gigabyte-sized files, as well... - Egon Willighagen

Comments and questions *most* welcome... or requests for a hands-on on how to write plugins... did you know we have a SDK allowing you to skip the ground work of setting up a new plugin, and focus on the Java code implementing your functionality? - Egon Willighagen

Maybe he should start blogging :) - Egon Willighagen

Another example of a good unintended consequence of using ONS in undergraduate lab courses. He is a star student and did outstanding work. Clearly has a successful research career ahead of him. It's only anecdotal evidence, but I have to think that the fact that he's linking to his ONS coursework means that he's likely to be more open with his future research (when he's able to). - Steve Koch from Bookmarklet

Steve - I think your guidance is right on track. Those who are learning to work openly (to whatever degree) are at a significant advantage for finding positions with groups who value that approach - but they are also qualified for traditional "closed" positions with the added benefit of being able to show their potential future employer what they are capable of doing in their public... more... - Jean-Claude Bradley

I heard of warfarin having functional implications due to tautomerism, did you checked that ? - Khader Shameer

Ah, sorry... did not realize it was a book :( - Egon Willighagen

#2 bestseller in modeling and simulation: http://www.amazon.com/gp... - Andrew Lang

Andy it shows up as #7 for me from your link - Jean-Claude Bradley

#8 for me ... we seem to be dropping :( - Egon Willighagen

When number of new articles per check exceeds certain amount, NCBI provides only links. - Pawel Szczesny

ah, ok. Thanks Pawel. - Pierre Lindenbaum

See MyExperiment.org: http://www.myexperiment.org/workflo... - Egon Willighagen

quote: "What's the Tanimoto similarity of aspirin to Dr. Scholl's Wart Remover?" :) - Egon Willighagen

Does this use standard tables? ctable output would be nice - Rajarshi Guha

tabular at the moment, but certainly there will be room for customizations... this will not hit Bioclipse 2.2, but should make 2.4... - Egon Willighagen

You might have a look at the OpenTox project, which is setting up Open Specifications for releasing QSAR and toxicity data sets. - Egon Willighagen

Steve, what is the scope of your QSAR definition? Just binding affinity, or any chemical or biochemical acitivity? - Egon Willighagen

BTW, got an answer for: http://stackoverflow.com/questio... ? - Egon Willighagen

Free as in free beer, correct? How much is free, as in freedom? - Egon Willighagen

Wondering if any seriously large database has experience with making it an open project? - Egon Willighagen

For example, by crowd sourcing curation, allowing replications, streamlining sending around updates, etc... - Egon Willighagen

... and find fails on the fly. BTW, it does not actually save the CML. - Egon Willighagen

Can't wait for the street view version! - Egon Willighagen

Try NCBI's MINiML. It has TSV between Data-Table tags. And you were joking :-) - Neil Saunders

I've seen this in cheminformatics too: where a plain text format was wrapped in 2 XML tags to make it XML :) - Egon Willighagen

Ah, just like in Bioclipse! :) - Egon Willighagen

No RSS feed for the news :( - Egon Willighagen