June 2016 - cctbxbb - phenix-online.org

Project Scientist positions for computational methods
by Nicholas Sauter 13 Jun '16

13 Jun '16

Two Project Scientist positions are available in my group in the *Molecular Biophysics and Integrated Bioimaging* <http://biosciences.lbl.gov/divisions/mbib/> (MBIB) Division at Lawrence Berkeley National Lab. *Bioimaging Project Scientist* Position Summary: We have an exciting opportunity for a Bioimaging Project Scientist who will apply neuromorphic computing techniques to structural biology problems in X-ray diffraction, CryoEM, and CryoET. This will be a cross-disciplinary effort between MBIB and the Computational Research (CRD) Division at Lawrence Berkeley National Laboratory. The research group will include investigators Nick Sauter (X-ray Crystallography), Karen Davies (CryoEM/ET), and Chao Yang (Scalable Solvers). Specific Responsibilities: - Investigate how to apply deep learning algorithms to specific data processing and data interpretation problems in structural biology. - Implement convolutional neural network (CNN) code on neuromorphic computing hardware such as the IBM TrueNorth chip. Example problems include the identification of positive diffraction events in X-ray free-electron laser diffraction, conformational classification in CryoEM single particle reconstruction, and the identification of 3D sections for CryoET subtomogram averaging. - Use tools such as MatConvNet, CAFFE, THEANO or TensorFlow to construct and train CNNs that can be used to optimally classify experimental data. Required Qualifications: - Research experience in Structural Biology, with expertise in allied fields such as Bioinformatics, Mathematics, Computer Science, or Engineering (Ph.D. + 3 years or equivalent) - Strong background in image analysis and machine learning, including neural networks. - Working knowledge of image classification and/or other image processing techniques. - Proficient programming skills in MATLAB and/or Python. - Working knowledge of performance optimization for scientific codes. *Algorithm Developer Project Scientist* Position Summary: We are seeking an algorithm developer for the increasingly complex analysis of large diffraction datasets in structural biology. Current projects utilize XFEL crystallography and spectroscopy to investigate the photosynthetic mechanism of water splitting and to probe other metalloenzyme reactions. We also wish to test whether diffuse scattering can reveal correlated atomic motions in crystals. Many problems remain to be solved, including the details of how to optimally merge datasets from thousands of crystals. Our software development projects (including packages such as DIALS <http://dials.lbl.gov/> and cctbx.xfel <http://cci.lbl.gov/xfel>) have been highlighted in several high-impact publications listed HERE <http://biosciences.lbl.gov/profiles/nicholas-sauter>. Specific Responsibilities: - Continue work on the DIALS data integration suite. - Test new algorithms for optimally characterizing and merging data from serial crystallography experiments. - Analyze anomalous scattering from metalloenzymes using XFEL diffraction. - Investigate whether diffuse scattering can reveal correlated atomic motions in crystals. Required Qualifications: - Expertise in one or more computational techniques including, but not limited to, ray tracing to test underlying physical models of the diffraction, Bayesian approaches for refining model parameters, macromolecular modeling and refinement, neural networks for interpreting image features, as well as signal processing and denoising methods. - Extensive data analysis experience in crystallography or from more general bioimaging backgrounds are welcome. - We particularly encourage strong mathematical intuition and a track record of bringing new ideas and tools to fruition, as evidenced through written publication and clear presentation. Candidates should send an expression of interest, CV, and list of three references to Nick Sauter, nksauter(a)lbl.gov*. *Further details are posted at https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=82554. Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720

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Not wishing to raise this again but...
by R. D. Oeffner 13 Jun '16

13 Jun '16

Switching to git for the cctbx would be very liberating for developing and testing code I believe. If bisecting git hash values seems cumbersome one can always tag each commit with the number of previous commits made to the branch used for the build. These numbers are sequential and obviously straightforward to use for bisecting. We do this currently for the phaser git repo: https://git.csx.cam.ac.uk/x/cimr-phaser/phaser.git Rob Date: Mon, 13 Jun 2016 21:24:58 +0000 From: <richard.gildea(a)diamond.ac.uk> To: <cctbxbb(a)phenix-online.org> Subject: Re: [cctbxbb] Not wishing to raise this again but... Message-ID: <1BB183A24316FD4DA62A5F8B952D4291CC715321@exchmbx03> Content-Type: text/plain; charset="windows-1252" At least according to Google Trends, svn has been on a downward trend since about 2009/10, whereas git is still firmly on an upward trend (and overtook svn in popularity long ago): <https://www.google.co.uk/trends/explore#q=git%20commit%2C%20svn%20commit&cm…> https://www.google.co.uk/trends/explore#q=git%20commit%2C%20svn%20commit&cm… <https://www.google.co.uk/trends/explore#q=git%20commit%2C%20svn%20commit&cm…><https://www.google.co.uk/trends/explore#q=git%20commit%2C%20svn%20commit&cm…><https://www.google.co.uk/trends/explore#q=git%20commit%2C%20svn%20commit&cm…> [cid:162fa876-cc25-6335-73af-714b0957d71e] I think that avoiding a move to git is simply delaying the inevitable (and if the cctbx didn't ever move with the times then we'd still be stuck with CVS). In my opinion, the potential benefits to using git far outweigh the (slightly) added complexity. <https://www.google.co.uk/trends/explore#q=git%20commit%2C%20svn%20commit&cm…><https://www.google.co.uk/trends/explore#q=git%20commit%2C%20svn%20commit&cm…>Cheers, Richard ________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of Nicholas Sauter [nksauter(a)lbl.gov] Sent: 13 June 2016 22:05 To: cctbx mailing list Subject: Re: [cctbxbb] Not wishing to raise this again but... I'd vote against the switch to git. Simple things, like svn update [remote directory] seem too complicated. As for slightly involved tasks like code bisection to locate the past commit that broke the test, well....I've never been able to figure this one out so I am pretty lost trying to debug DIALS. I do not wish to make things difficult for the maintenance of cctbx.xfel. Nick Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720 (510) 486-5713 On Mon, Jun 13, 2016 at 8:52 AM, Luc Bourhis <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: On 13 Jun 2016, at 17:09, Graeme.Winter(a)Diamond.ac.uk<mailto:[email protected]> wrote: ? is there any enthusiasm out there for moving cctbx to git? The more I work with git the more I wish this existed properly for cctbx. I?ve raised this a bunch of times and always it is ?not right now? however ?a good idea? ? this?ll be the last time I ask? Could we move to git, please? I note the bootstrap script for Windows now has a git dependency even! +1 ? and time to share some thoughts! It would be great if we could get the cctbx up and running by just cloning, configuring and building without needing to download anything else. That could be done by adding SCons, Boost, and ccp4io as submodules in the cctbx repository. And I reckon ccp4io_adaptbx should be added as a subtree since it is developed by the same people as the cctbx. Just an idea to think about as I haven?t not worked out the details at all. Best wishes, Luc _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/cctbxbb -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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XQuartz 2.7.9 issue for OS X
by Billy Poon 10 Jun '16

10 Jun '16

Hi all, There seems to be an issue with XQuartz 2.7.9 on OS X when trying to render an OpenGL window (e.g. Coot, PyMOL, Phenix GLViewer) over SSH using X forwarding (i.e. ssh -Y). You will get an error that looks like X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) It seems like indirect rendering of a GLX context does not work properly on 2.7.9. Downgrading to XQuartz 2.7.8 works for me. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Who is using bootstrap.py on Windows?
by Robert Oeffner 10 Jun '16

10 Jun '16

Hi all, I would like to know if there are teams other than Phenix and Dials-west in Berkeley doing regular builds on Windows using cctbx_project/libtbx/auto_build/bootstrap.py. I plan to make some simplifications of this script using the ssh client that is part of Git for Windows rather than the one found in the PuTTY suite which we use currently. Many thanks, Robert

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Berkeley Server Downtime (6/3/2016)
by Billy Poon 01 Jun '16

01 Jun '16

Dear all, On Friday, June 3, our servers will be shutdown starting at 6:30 am Pacific for scheduled maintenance in our building (7 - 8 am). This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) We expect that the servers will be available by 8:30 am Pacific at the latest. Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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