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[SA_Scat] Year in Industry placement at Diamond Light Source -Harnessing Cluster Computing for Scientific Data Analysis via Web Services

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  • Subject: [SA_Scat] Year in Industry placement at Diamond Light Source -Harnessing Cluster Computing for Scientific Data Analysis via Web Services
  • From: <stephen.king@stfc.ac.uk>
  • Date: Tue, 24 Oct 2017 09:36:28 +0000
  • Accept-Language: en-GB, en-US
Harnessing cluster computing for scientific data analysis via web facing database servicesDiamond year in industry placement, 2018
Apply online: http://extranet2.diamond.ac.uk/ISV/StudentPortal/SandwichPlacement.aspxApplications accepted until the 10th of November 2017

The synchrotron at Diamond Light Source facilitates access to a variety of techniques for analysing matter, ranging in complexity from ideal, model systems through to real-world applications. This broad spectrum of analytical techniques presents a unique challenge; the unification of many different, disparate, software packages to work together in unison providing our users with the information they desire, as quickly as possible.
At Diamond we offer the use of a web-facing application called SynchWeb that interfaces with a database system entitled the Information System for Protein CrystallographY Beamlines, or ISPyB, to present users with their data remotely. This application also provides our users with data provenance, information management and an electronic log-book alongside access to results from a growing number of tools for data analysis integrated within the SynchWeb/ISPyB infrastructure.
Currently the Small Angle X-ray Scattering (SAXS) community is poorly catered for in SynchWeb with few, if any, analysis tools available to our user base. The main goal of this project is to integrate the functionality of the open source program SasView into SynchWeb. This will provide our users with information on the size and shape of nano- to micro- sized objects in solution both during and after their experiments.
In order to achieve this, it will be necessary to work with the SasView and SynchWeb development communities to complete development of headless versions of SasView and to extend SynchWeb to communicate with SasView. The results will be recorded in the standardised Neutron, X-ray, and muon Science (NeXus) file format using the NeXus collective action for nomadic Small Angle Scatterers (NXcanSAS) application standard allowing for ingestion into the ISPyB database, this will also require extending ISPyB for NXcanSAS.
There is also potential to expand the project in one of two ways; firstly by incorporating the functionality of another data analysis package, McSAS, into the SynchWeb/ISPyB infrastructure further utilising the NeXus and NXcanSAS standards. Or, secondly, by simulating experimental results, informing users about what information to expect from their samples as well as providing seed information for downstream machine learning algorithms.
As this project aims to unify multiple software packages together there is a strong element of collaboration present, both with colleagues inside Diamond as well as national and international partners. Additionally, in order to gain familiarity with SAXS as an analytical technique, there will also be an element of visiting user groups, as they conduct their experiments at Diamond, to gain insight into what analyses are being performed and why. Towards the end of the project there will also be opportunities to present the resulting work at relevant workshops or conferences.
Project goals
Collaborate with the SasView developer community to:
* Aid completion of headless, or server, versions of SasView* Improve and enhance the functionality of SasView, preferentially for the x-ray community* Verify, and if necessary complete, implementation of NXcanSAS application standard within SasView

Work with the SynchWeb and ISPyB developer communities to:
* Develop functionality to read results given in the NXcanSAS format from SasView into SynchWeb via ISPyB* Build a web-facing front end to display results obtained from SasView in SynchWeb* Integrate SynchWeb and ISPyB with SasView to facilitate the analysis of obtained results, reprocessing of results

Integrate into the Diamond and SAXS communities by:
* Communicating with Diamond users and beamline staff to understand the experiments conducted andanalysis expectations* Collaborating with the DAWN programming team at Diamond to ensure NXcanSAS compliance and understand the data produced* Taking part in relevant training courses and programs Demonstrate progress made by:* Sharing advances made with SasView, ISPyB and SynchWeb to Diamond staff, users and collaborators * Development of documentation and unit tests for software created* Dissemination of work at relevant workshops or conferences
Build on the project foundations to:
* Incorporate the functionality offered by McSAS into SynchWeb and ISPyB* Simulate results anticipated from experiments via SasView* Generate simulated data, and metadata, to provide seed data for downstream machine learning algorithms

Essential criteria
* Programming experience* Mathematical knowledge to an A-level, or equivalent, standard

Desirable criteria
* Python programming experience * Java programming experience* Knowledge of X-ray science* Web UI development experience * Database systems knowledge_______________________________________________sa_scat mailing listsa_scat@iucr.orghttp://mailman.iucr.org/cgi-bin/mailman/listinfo/sa_scat

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