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RDKit

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The 2015.03 release of the RDKit is now available.

The release can be found at github:
https://github.com/rdkit/rdkit/releases/tag/Release_2015_03_1.
Click through to see the release notes and download Windows binaries or the source distribution.

The DOI for this release is: http://dx.doi.org/10.5281/zenodo.17294

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****** Release_2015.03.1 ******* (Changes relative to Release_2014.09.2) !!!!!! IMPORTANT !!!!!! This release has a new algorithm for canonical atom ordering. This means that canonical SMILES generated with the new version will be different from those generated with previous versions. Acknowledgements: David Cosgrove, Andrew Dalke, JP Ebejer, Niko Fechner, Igor Filippov, Patrick Fuller, David Hall, J Bach Hardie, Jan Holst Jensen, Brian Ke...
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In next months rdkit will be soon pushed into Fedora / RHEL / CentOS / Scientific Linux repositories. Thanks to Gialuca Sforna and Rex Dieter
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Save the date: 2015 RDKit UGM

This year's RDKit UGM will be hosted by Sereina Riniker at the ETH in Zurich, Switzerland. The meeting will take place on the 2nd and 3rd of September, with a hackathon day on the 4th.

The call for contributions and more detailed information about the meeting will come out later in Q1, but we wanted to make sure everyone can mark their calendars as soon as possible.

Many thanks to Sereina for taking on the task of hosting this year's UGM!
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Here's the agenda for next week's RDKit UGM.

I can't wait! :-)

#rdkitugm2014  
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The calculation of pairwise compound similarities based on fingerprints is one of the fundamental tasks in chemoinformatics. Methods for efficient calculation of compound similarities are of utmost importance for various applications like similarity searching or library clustering.
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A fully functional port of the #RDKit  to Python3 is now available on this branch:
https://github.com/rdkit/rdkit/tree/python3-support

We'll be merging this onto the trunk in about a week, but early feedback would be very welcome.
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Epidemiological studies in the recent years have investigated the relationship between dietary habits and disease risk demonstrating that diet has a direct effect on public health. Especially plant-based diets -fruits, vegetables and herbs- are known as a source of molecules with pharmacological properties for treatment of several malignancies. Unquestionably, for developing specific intervention strategies to reduce cancer risk there is a need f...
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#rdkitannouncement   
I'm pleased to announce that the next version of the RDKit -- 2014.03
(a.k.a Q1 2014) -- is released.

The release notes are here:
https://github.com/rdkit/rdkit/releases/tag/Release_2014_03_1

The release and binary files are on the github release page:
https://github.com/rdkit/rdkit/releases/tag/Release_2014_03_1
as well as the sourceforge downloads page:
http://sourceforge.net/projects/rdkit/files/rdkit/Q1_2014/

I have uploaded 32-bit and 64-bit Windows binaries for Python 2.7 and, in response to a couple of requests, 32-bit and 64-bit Windows binaries for Java.

The online version of the documentation at rdkit.org has been updated.

Thanks to the everyone who submitted bug reports and suggestions for this release!

Please let me know if you find any problems with the release or have suggestions for the next one, which is scheduled for September 2014.
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This year's RDKit User Group Meeting will take place from 2-4 September at the ETH Zurich, Switzerland. Sereina Riniker will be hosting the event. Thanks Sereina!

Registration for the RDKit UGM is free: https://www.eventbrite.com/e/4th-rdkit-user-group-meeting-tickets-15827426258

The previous years' format seemed to work pretty well and the feedback was positive, so we will stick to the same format this year:

Days 1 and 2: Talks, lightning talks, roundtable(s), discussion, and talktorials. For those who haven’t attended before, talktorials are somewhere between a talk and a tutorial, they cover something interesting done with the RDKit and include the code used to do the work. During the presentation you'll give an overview of what you did and also show the pieces of the code that are central to the work. The idea is to mix the science up with the tutorial aspects.

Day 3 will be a sprint: those who choose to stay will spend an intense day working in small groups to produce useful artifacts: new bits of code, KNIME nodes, knime workflows, tutorials, documentation, IPython notebooks, etc. We will once again try to structure this a bit by collecting a bunch of ideas for things to work on in advance.

There will also be, of course, social activities.

Cooperation with KNIME: Something new this year: our friends at KNIME will be participating in the meeting. If there’s sufficient interest, they have also agreed to offer a one-day KNIME course on the Tuesday before the UGM (the 1st of September). If you're interested and believe you will be able to attend please indicate this when you register.

The registration page and announcement (http://www.rdkit.org/RDKitUGM2015Announcement.pdf) contain additional information about hotels and logistics.

We are looking for people who are willing to do presentations or talktorials on the first two days. If you're interested in contributing, please send Sereina and I email. Lighting talks don't need to be arranged too far in advance; we will start collecting the list of people interested in doing those shortly before the event.

#rdkitannouncement  
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The 2014.09.1 (Q3 2014) version of the RDKit is now available.

The release can be found at github (https://github.com/rdkit/rdkit/releases/tag/Release_2014_09_1) or sourceforge (http://sourceforge.net/projects/rdkit/files/rdkit/Q3_2014/). Click through to see the release notes and download Windows binaries or the source distribution.

New this time, there is now a DOI available for the RDKit via zenodo: http://dx.doi.org/10.5281/zenodo.12483

#rdkitannouncement  
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+Gianluca Sforna has created binary RPMs for Fedora 20, 21 and RHEL/Centos 6, 7 that are available from:
https://copr.fedoraproject.org/coprs/giallu/rdkit/ 
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A database searching approach can be used for metabolite identification in metabolomics by matching the measured tandem mass spectra (MS/MS) against the predicted fragments of metabolites in a database. Here we present the open-source MIDAS algorithm (Metabolite Identification via Database ...
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No, that functionality is not available.
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Open source cheminformatics and machine learning