[ccp4bb] Software Engineer (Web Development) for ISPyB and SynchWeb at Diamond.

[Alun Ashton]

Please find enclosed details for a new developer role on Synchweb and ISPyB at 
Diamond Light Source.

http://www.diamond.ac.uk/Careers/Vacancies/All/139_17_CH.html 
Job Title: Software Engineer (Web Development) 
Post Type: Full-time, 2 year Fixed Term Contract 
Salary information:  £32,805 to £38,593 (Discretionary range to £44,382)
Application deadline: 18/02/2018

The role will work as part of a small dedicated team working towards full 
experiment information management across the whole of the facility but 
especially within the life science domain. The work will also involve 
collaborating closely with international partners. 

Further details on SynchWeb and ISPyB available at:
http://diamondlightsource.github.io/SynchWeb/ 
http://www.diamond.ac.uk/Beamlines/Mx/I03/I03-Manual/Using-ISPyB.html 
https://ispyb.github.io/ISPyB/

Further details and other opportunities available at: 
http://www.diamond.ac.uk/Careers/Vacancies.html 

Alun
___
Alun Ashton, alun . ash...@diamond.ac.uk Tel: +44 1235 778404
Group Leader - Data Analysis Software,    www.diamond.ac.uk 
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.



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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

[ccp4bb] Diamond Webinar - The Changing Landscape of MX - 25th January

[Alun Ashton]

Dear All,

Apologies to those of you who will have received this already but it's been 
suggested that this could be of interest to the general ccp4bb members:
--

Diamond is pleased to present its fourth monthly Synchrotron User Webinar. This 
webinar is aimed at the User Community from PIs to students. It will be 
broadcast live online and will allow viewers to submit questions to be 
discussed.

This month's webinar is on Thursday 25th January 2018 at 16:00 (UTC, London 
time).  The topic will be 'The Changing Landscape of MX' brought to you by the 
Principal Beamline Scientist of VMXi (Thomas Sorensen) and the Principal 
Beamline Scientist of I23 (Armin Wagner).

We invite you to register for this webinar by clicking 
here<http://www.diamond.ac.uk/Home/Events/Webinars/2018/landscape-of-mx-4/Register.html>.
 This will enable us to contact you closer to the date with the necessary 
viewing link.

Starting at 16:00
- Welcome and introductions - Chairperson - Laura Holland
- VMXi<http://www.diamond.ac.uk/Beamlines/Mx/VMXi.html> beamline update - 
Principal Beamline Scientist of 
VMXi<http://www.diamond.ac.uk/Beamlines/Mx/VMXi.html> - Thomas Sorensen
- I23<http://www.diamond.ac.uk/Beamlines/Mx/I23.html> beamline update - 
Principal Beamline Scientist of 
I23<http://www.diamond.ac.uk/Beamlines/Mx/I23.html> - Armin Wagner
- Discussion - Panel: T. Sorensen and A. Wagner
- Upcoming available training and events in MX and conclusions - Chairperson - 
Laura Holland

Ending by 17:00

The above information can also be found 
here<http://www.diamond.ac.uk/Home/Events/Webinars/2018/landscape-of-mx-4.html>.

The webinar will be delivered live only - recordings will not be available 
after the event.

Kind regards,

The Webinar Team
Email: webin...@diamond.ac.uk<mailto:webin...@diamond.ac.uk>

---



Alun

_______

Alun Ashton, alun.ashton@ diamond.ac.uk Tel: +44 1235 778404

Group Leader - Data Analysis Software,www.diamond.ac.uk

Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.





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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

[ccp4bb] Data analysis for Electron Microscopy, Machine Vision, and Team Leader positions at Diamond Light Source

[Alun Ashton]

Dear All,

Please find enclosed details of positions with the Data Analysis Group at 
Diamond Light Source:

Job Title: Data Analysis Scientist / Senior Software Scientist - Electron 
Microscopy
Post Type: Full time / 3 year Fixed Term Contract
Salary information: £32,805 to £38,593 (Discretionary range to £44,382) / 
Senior role: £42,297 to £49,761 (Discretionary range to £57,225)
Application deadline: 07/01/2018 
http://www.diamond.ac.uk/Careers/Vacancies/All/129_17_CH.html 

Job Title: Data Analysis Scientist - Machine Vision
Post Type: Full time / 3 year Fixed Term Contract
Salary information: £32,805 to £38,593 (Discretionary range to £44,382) 
Application deadline: 07/01/2018
http://www.diamond.ac.uk/Careers/Vacancies/All/128_17_CH.html   

Job Title: Senior Software Engineer - Team Leader
Post Type: Full time / Permanent
Salary information: £42,297 to £49,761 (Discretionary range to £57,225)
Application deadline: 07/01/2018
http://www.diamond.ac.uk/Careers/Vacancies/All/130_17_CH.html  

Further details and other opportunities available at: 
http://www.diamond.ac.uk/Careers/Vacancies.html  

Alun
___
Alun Ashton, alun.ashton @ diamond.ac.uk Tel: +44 1235 778404
Group Leader - Data Analysis Software,www.diamond.ac.uk 
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.



-- 
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

Re: [ccp4bb] Implementation of the ESRF Data Policy

[Alun Ashton]

Dear Adrian,

Although the thread has moved on, one clarification on your comparison to 
Diamond’s data policy, Although Diamond does archive all YOUR data from peer 
reviewed research  (note no distinction between raw and processed), according 
to our terms or usage we do not make that data open access.

The current status was recently reviewed and presented to Diamond User 
Committee (DUC) with the below slides and I believe was recently summarised by 
John Helliwell at a recent BCA meeting as part of a broader overview.
https://www.dropbox.com/s/q7twrbodmv3cqmr/160309%20Current%20archive%20status%20at%20Diamond.pdf?dl=0

The policy is under constant review and we encourage Diamond users to send 
their feedback (support or objections) e.g. via their DUC representative.

The relevant links:
Diamond Experiment Data Management Policy:
http://www.diamond.ac.uk/Users/UserGuide/Data-User-Guide/Accessing-Data/Data-Policy.html

Diamond User Committee
http://www.diamond.ac.uk/Home/Company/Management/DUC.html



From: Adrian Goldman [mailto:adrian.gold...@helsinki.fi]
Sent: 08 April 2016 11:09
Subject: Re: Implementation of the ESRF Data Policy

Xavier,

  As far as I am aware, this brings the ESRF policy in line with eg the 
policy at Diamond.  I mostly agree with you; and anyway the current policy 
being implemented certainly in the UK of keeping everything for 10 years is I 
think ridiculous: most of the data that we collect is completely useless.  
Sadly.

  I was at the ESRF council meeting where this was discussed, and there 
was to the best of my recollection very little enthusiasm for other proposals.  
In addition, I think a little bit of misdirection in ones naming and data 
collection strategy will suffice to make sure that the
data collected is not actually usable by a competitor lab, unless they happen 
to have exactly the same crystal form, same construct etc as you.  As such 
misdirection is also already prevalent in high-impact factor papers, plus other 
small acts of malfeasance, like sending out
clones that do _not_ correspond to the ones reported in the literature, I am 
sure it will not be beyond one’s wit to come up with similar strategies for 
data at the beamline.

  I am by no means condoning such behaviour, nor do I do it: I have 
merely noticed it in others and what they publish/have sent us.

  For obvious reasons, 
I am not going to name names.


  Adrian

ps: The larger question surely is what societal purpose is served by this level 
of competition? My feeling is: not much.

On 8 Apr 2016, at 12:47, F.Xavier Gomis-Rüth 
> wrote:

Dear CCP4ers,
I received the message below from the ESRf User Office some weeks ago and was 
wondering if others within the community had, too, and would
put this up for discussion within the BB. But as this is apparently not the 
case, I will come to the fore ;-) .
I must say this is a unilateral decision by ESRF, I was completely unaware that 
this was under discussion. While I am truly not against
transparency, in particular in the case of publicly funded research, in this 
case I consider that things have simply gone too far. A really challenging
project in MX currently ALWAYS takes more than 3 years to be published after 
the very first dataset was collected, so this regulation poses an
additional, completely artificial and gratuitous pressure on researchers to 
finish everything within a determined and clearly too short time span.
Another font of unnecessary pressure is provided by some journals, such as 
NSMB, which now impose that not only the coordinates be send for review of a 
manuscript but rather the cif files with the reflections, while, obviously, 
reviewers keep their anonymity. Given the particular characteristics of our 
field, where
who publishes first irreversibly relegates competitors to the absolute 
irrelevance, such policies rather favor fraud but on the other side, on that of
potentially desperate competitors, whose very existence depends on relevant 
publications and who easily could take advantage of this information.
While sound cases of fraud, historical and recent, clearly impose the necessity 
of stringent control, this must happen in a rational way and following
consensus within the community, which has not happened in the aforementioned 
cases. In the case of ESRF, this could be easily accomplished as in the PDB,
where data are released upon publication. In the case of journals, by 
performing an exhaustive verification of structures AFTER the manuscript has 
been
pre-accepted, as a final condition for definitive acceptance.
I would be very interested in the opinion of the BB.
Best,
Xavier


 Forwarded Message 
Subject:

Implementation of the ESRF Data Policy

Date:

Mon, 29 Feb 2016 

Re: [ccp4bb] Off-topic: Transfering data from Diamond

[Alun Ashton]

Since all Diamond data is archived onto tape it is also available at 
http://icat.diamond.ac.uk  (at the latest the following Tuesday) and ordered 
based on directory name which are referred to as datasets. It's not necessarily 
the easiest GUI, and large downloads can be slow at best, but a replacement is 
in beta testing. For large datasets if they are still on our disks there is 
also a Globus GridFTP end point again in beta testing which can sometimes 
_greatly_ speed up data transfer, we can send details offline if interested.

Alun
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Group Leader - Data Analysis Software,www.diamond.ac.uk 
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.

 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 David Hall
 Sent: 31 July 2015 11:23
 To: ccp4bb
 Subject: Re: [ccp4bb] Off-topic: Transfering data from Diamond
 
 We'd much rather you connected to Diamond and pushed data back though:
 
 http://www.diamond.ac.uk/Beamlines/Mx/Common/Common-
 Manual/Data-Backup/Remote-Backup.html
 
 Thanks
 
 Dave
 
 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Jonathan Davies
 Sent: 31 July 2015 11:20
 To: ccp4bb
 Subject: Re: [ccp4bb] Off-topic: Transfering data from Diamond
 
 You can SSH to diamond using the host: nx.diamond.ac.uk
 
 Jonathan
 
 On 30/07/15 23:00, Mohamed Noor wrote:
  Dear all
 
  I have about 70 folders of data collected at Diamond. As I only want to keep
 about 50 of them, is there a script that can read in the folder names from a
 text file and download those?
 
  Normally, I use FileZilla but it gets tedious to click so many times after a
 while
 
  Secondly, some folders have one sweep of data, some others with two or
 even three, is it possible to run a command from terminal that will filter
 different sweeps and output the number of frames?
 
  For example, in a folder with files:
 
  _sweep1_0001.cbf - _sweep1_1800.cbf _sweep2_0001.cbf -
  _sweep2_0900.cbf
 
  I want to get a text file output containing a line saying:
  /folder/name/sweep1 - 1800
  /folder/name/sweep2 - 900
 
  The idea is so that I can feed those lines into XDS.INP without checking how
 many sweeps there are in each folder and how many frames.
 
  I'm pretty sure someone on the BB has a trick for this.
 
  Thanks.
 
 
 --
 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

-- 
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

[ccp4bb] PDRA opportunity in crystallography software methods development at Diamond Light Source

[Alun Ashton]

We are looking for a high calibre PDRA/software scientist to join our 
scientific software group to work on the development and optimisation of 
existing automated crystallography data processing software and algorithms and 
their application on new crystallographic problems, especially small molecule 
data processing. 

Full details can be found here:
http://www.diamond.ac.uk/Careers/Vacancies/All/DIA0920_CH.html  

Regards,
Alun
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Group Leader - Data Analysis Software,www.diamond.ac.uk 
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.





-- 

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

 

[ccp4bb] Data Analysis Scientist Post at Diamond Light Source

[Alun Ashton]

We are looking for a high calibre software scientist to join our scientific 
software group to work on visualization and analysis of diffraction and 
spectral data. The group have the responsibility for the provision of advanced 
data evaluation, analysis and visualization software applications for users of 
Diamond.

Full details can be found here:
http://www.diamond.ac.uk/Home/Jobs/Current/DIA0905_CH.html 

Regards,
Alun
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Group Leader - Data Analysis Software,www.diamond.ac.uk 
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.





-- 

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

 

[ccp4bb] Summer Student Placements @Diamond

[Alun Ashton]

Dear All,

I would be grateful if you could bring the enclosed/linked opportunity to the 
attention of any suitable candidates in your institutions. Please also 
encourage them to look at all the categories e.g. the computing category is a 
bit of a misleading label (that might change soon). 

The Diamond Student Summer Placement scheme allows undergraduate students 
studying for a degree in Science, Engineering, Computing or Mathematics (and 
who expect to gain a first or upper-second class honours degree) to gain 
experience working within a scientific environment at Diamond. These 8-12 week 
placements are paid positions and will provide successful students with an 
opportunity to work on a research or development project within Diamond.

http://www.diamond.ac.uk/Home/Jobs/placements/Current.html 

Sent on behalf of the placement organisers. 
Alun



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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

 

[ccp4bb] PhD studentship in Biological Image Analysis

[Alun Ashton]

(Full details at http://www.nottingham.ac.uk/jobs/currentvacancies/ref/SCI1278)

Applications are invited for a fully-funded PhD studentship to be held jointly 
at the School of Computer Science, University of Nottingham and The Diamond 
Light Source, the UK's national synchrotron facility at Harwell, Oxfordshire. 
Diamond generates brilliant beams of light from infra-red to X-rays which are 
used to acquire images at extremely high resolutions: imaging of sub-cellular 
components of biological objects is a key application of the Diamond facility. 
Analysis of such images requires cell components to be identified and accurate, 
quantitative descriptions of their properties (shape, size, position, etc) 
recovered from the image. The very high spatial and grey-level resolution of 
synchrotron images means that very fine details (of e.g. mitochondria) are 
visible - organelles do not appear as simple, evenly coloured regions but as 
highly variable, textured areas. This PhD project seeks to develop automatic 
image analysis methods and software tools that can extract quantitative 
measurements of sub-cellular objects from Diamond Light images. The successful 
student will work closely with research staff and potential users at both 
Nottingham and Diamond.
 
Students should have a good first degree (preferably at the level of a 
first-class degree in the UK context) in Computer Science or a related 
discipline. Previous experience of image analysis, computer vision or 
biological science are an advantage, but not essential. 
 
Informal enquiries may be addressed to:
 Dr Andrew French: andrew.p.french @ nottingham.ac.uk
 Dr Mark Basham: Mark.Basham @ diamond.ac.uk
 Dr Tony Pridmore: tony.pridmore @ nottingham.ac.uk
 
Details on how to apply are on the website. 

Alun Ashton
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Group Leader - Data Analysis Software,www.diamond.ac.uk 
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.





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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

 

Re: [ccp4bb] a new version of XDS

[Alun Ashton]

Graeme is away this week but was working on the problem before he went away. 
Looking at his update on the XIA2 blog it does look like at least the SVN 
version of XIA2 should be ok, older versions/releases of XIA2 are unlikely to 
work.

Alun
___
Alun Ashton, alun.ash...@diamond.ac.ukmailto:alun.ash...@diamond.ac.uk Tel: 
+44 1235 778404
Scientific Software Team Leader,  http://www.diamond.ac.uk/
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Sebastiano Pasqualato
Sent: 30 May 2013 07:55
To: ccp4bb
Subject: Re: [ccp4bb] a new version of XDS


Hi Folmer,
it's just a matter of time, you know, given the short-living license of XDS. ;-)

Anyway, I second the request,
ciao,
s


On May 30, 2013, at 8:50 AM, Folmer Fredslund 
folm...@gmail.commailto:folm...@gmail.com wrote:


Hi all,
Nice with a new version (I guess that means improvements :-)
Before I upgrade, I just have one question:
Does the change in the XPARM.XDS format mean that software such as xia2 will be 
broken?
Thanks,
Folmer

2013/5/29 Kay Diederichs 
kay.diederi...@uni-konstanz.demailto:kay.diederi...@uni-konstanz.de
... is available for academic users at 
http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/
Please note that there are some incompatibilities; most notably, the new format 
of XPARM.XDS is different so that the new INTEGRATE does not work with an old 
XPARM.XDS.

best,

Kay



--
Folmer Fredslund

--
Sebastiano Pasqualato, PhD
Crystallography Unit
Department of Experimental Oncology
European Institute of Oncology
IFOM-IEO Campus
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990








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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

 

[ccp4bb] Software Development Posts at Diamond

[Alun Ashton]

Please find details below details of software development posts at Diamond. 
Full details on these posts and others can be found on the web site 
http://www.diamond.ac.uk/Home/Jobs/Current.html.

MX and BioSAXS Automation
-
Job Title: Software Engineer  
Post Type: Full Time- Fixed Term- 3 years 
Salary information Circa £33k 
Job Reference: DIA0789/CG  
http://www.diamond.ac.uk/Home/Jobs/Current/DIA0789_CG.html   
Application deadline 30/11/2012 
The successful candidate will contribute to our efforts in software automation 
in the field of structural biology. In particular, macromolecular 
crystallography (MX) and biological small angle X-ray scattering techniques 
(BioSAXS), two highly automated, complementary experiments used to determine 3 
dimensional structural information on proteins. Working with existing staff and 
international collaborators you will enhance and extend our existing fully 
automatic MX data reduction and structure solution pipelines as well as help 
develop the equivalent for BioSAXS as part of a European wide initiative, 
Biostruct-X (http://www.biostruct-x.eu/).

MX Data Acquisition
---
Job Title: Software Scientist  
Post Type: Permanent/ Full Time 
Salary information Circa £33k 
Job Reference: DIA0774/CB  
http://www.diamond.ac.uk/Home/Jobs/Current/DIA0774_CB.html  
Application deadline 16/11/2012 
Duties to include:
* Share the first line support of the software for MX interacting closely with 
both beamline staff and external users;
* Participate in the implementation of the data acquisition software for one or 
more Diamond beamlines under the mentoring of more senior group 
members.(Initially for MX);
* Use particular scientific experience to participate actively in the use and 
direct support of Diamond's Macromolecular Crystallography (MX) beamlines first 
to establish requirements and then to manage the implementation of software to 
improve and extend functionality;

SR Data
---
Job Title: Software Engineer  
Post Type: Fixed Term- 1 year/ Full Time 
Salary information Circa £33k 
Job Reference: DIA0772/CB  
http://www.diamond.ac.uk/Home/Jobs/Current/DIA0772_CB.html  
Application deadline 16/11/2012 
Duties
* Implement  updated NeXus standard data format for data acquisition software 
where appropriate and participate in the development of supporting software 
within the Data Acquisition and Scientific Computing groups at Diamond; 
* Development of Eclipse RCP perspective and toolkit;
* Contribute to the provision of documentation  for software developed within 
the Data Acquisition and scientific computing groups at Diamond; 


Alun
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Scientific Software Team Leader,  http://www.diamond.ac.uk/
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.





-- 

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

 

[ccp4bb] Vacancy for Software Engineer: BioSAXS and MX automation

[Alun Ashton]

Dear All, 

Please see below details of a Software Engineer post available within the 
scientific software team at Diamond. 
It's not particularly obvious from the advertisement that the role will be to 
work with existing staff and collaborators to enhance and extend our existing 
fully automatic MX data reduction and structure solution pipelines as well as 
to help develop the equivalent for BioSAXS.

For full details please go to the web pages at:
http://www.diamond.ac.uk/Home/Jobs/Current/DIA0752_CG.html

Job Title: Software Engineer  
Job Reference: DIA0752/CG  
Post Type: Full Time- Fixed Term- 3 years 
Division: Science 
Salary information: Circa £33k 
Application deadline: 23/08/2012 
Date of interviews: TBC  


Informal enquaries can be made directly to me. 
Alun
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Scientific Software Team Leader,  http://www.diamond.ac.uk/
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.





-- 

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

 

[ccp4bb] Vacancy for a Data Analysis Scientist: Diffraction and crystallography

[Alun Ashton]

Dear All, 

Please see below details of a data analysis scientist post available within the 
scientific software team at Diamond. For full details please go to the web 
pages at:

http://www.diamond.ac.uk/Home/Jobs/Current/DIA0686-TH.html

Job Title: Data Analysis Scientist  
Job Reference: DIA0686/CG  
Post Type: Full time, permanent 
Division: Science 
Salary information: Circa £34k - a higher salary may be available for an 
exceptionally experienced and qualified candidate. 
Application deadline: 25/03/2012 

Regards,
Alun Ashton
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Scientific Software Team Leader,  http://www.diamond.ac.uk/
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.

Re: [ccp4bb] IUCr committees, depositing images

[Alun Ashton]

Sorry Matt, some large facilities do already keep all their raw and processed 
data. And I think the EU grant you mention to coordinate this is 
http://www.pan-data.eu  soon to be odi, includes the ESRF :), don't your 
computing people tell you anything ?! :)

PanData have a meeting in early November and they (ahem we) are already in 
touch with the working group and will formalise that soon after the meeting.

Alun
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Scientific Software Team Leader,  http://www.diamond.ac.uk/
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Matthew 
BOWLER
Sent: 26 October 2011 10:03
To: ccp4bb
Subject: Re: [ccp4bb] IUCr committees, depositing images

The archiving of all raw data and subsequently making it public is something 
that the large facilities are currently debating whether to do.  Here at the 
ESRF we store user data for only 6 months (and I believe that it is available 
longer on tape) and we already have trouble with capacity.  My personal view is 
that facilities should take the lead on this - for MX we already have a very 
good archiving system - ISPyB - also running at Diamond.  ISPyB stores lots of 
meta data and jpgs of the raw images but not the images themselves but a link 
to the location of the data with an option to download if still available.  My 
preferred option would be to store all academically funded data and then make 
it publicly available after say 2-5 years (this will no doubt spark another 
debate on time limits, special dispensation etc).  What needs to be thought 
about is how to order the data and how to make sure that the correct meta data 
are stored with each data set - this will rely heavily on user input at the 
time of the experiment rather than gathering together data sets for depositions 
much later.  As already mentioned, this type of resource could be extremely 
useful for developers and also as a general scientific resource.  Smells like 
an EU grant to me. Cheers, Matt.


On 26/10/2011 10:21, Frank von Delft wrote:
Since when has the cost of any project been limited by the cost of hardware?  
Someone has to implement this -- and make a career out of it;  thunderingly 
absent from this thread has been the chorus of volunteers who will write the 
grant.
phx





--

Matthew Bowler

Structural Biology Group

European Synchrotron Radiation Facility

B.P. 220, 6 rue Jules Horowitz

F-38043 GRENOBLE CEDEX

FRANCE

===

Tel: +33 (0) 4.76.88.29.28

Fax: +33 (0) 4.76.88.29.04



http://go.esrf.eu/MX

http://go.esrf.eu/Bowler

===

Re: [ccp4bb] IUCr committees, depositing images

[Alun Ashton]

Hi James,

1) thanks for sending and email in this thread longer than mine, I was 
worried I had killed it... ;)

2)  you say:
 Of course, if we are willing to relax the requirement of validation and
 curation, this could be a whole lot easier.  In fact, there is already
 an image deposition infrastructure in place!  It is called TARDIS:
 
 http://tardis.edu.au/
 
 Perhaps the best way forward would be for the PDB to introduce a new
 field for one or more TARDIS ids in a PDB deposition?  It would be
 optional at the first, but no doubt required in the future.

And Ethan has just beat me to this point, from the Tardis web site, first 
paragraph last sentence:
Storage was and remains federated, meaning the public index, TARDIS.edu.au 
contains no data itself and merely points to data stored in external labs and 
institutions.

So is the raw data even public? In that sense I think what were supposed to 
adopt in European facilities is ODI's which link accordingly to the facilities 
own suppository, and how that is developed and where you put it is down to 
regional preferences. It can obviously be large, small, publicly accessible, 
shared between friends or private. To be effective it will need to be around 
for a long time. 

But to build on the success of model for the 'PDB' I would agree that someone 
should pay to have someone host this, and at least in the first instance make 
sure PDB structures have their raw data available and accessible to all. Tardis 
is in the right direction as a catalogue, ICAT in the EU is a simpler DB, ISPyB 
would need a bit of work to get data sharable through the interfaces, but I 
think it is a richer data structure. 

Standardisation of the data would also be good, its amazing what a simple word 
checker can do to your emails these days

BTW we pay the equivalent to about a weeks beamtime on one beamline for 200TB a 
year data storage and access to it for the whole facility, and someone else to 
take the pain of hosting it 

Alun
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Scientific Software Team Leader,  http://www.diamond.ac.uk/
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.

Re: [ccp4bb] IUCr committees, depositing images

[Alun Ashton]

Sorry for my boring response………

‘Short’ bit:
Has anyone here considered DOI’s onto data? Facility sites within Europe and 
planning to make this available, I hope to do a proof of principle this year on 
data from Diamond (volunteers?). But as an example the ISIS neutron site on the 
same campus as us have started to do this, as a random example you can go to 
http://doi.org  and put in the DOI reference 10.5286/ISIS.E.24079772 (catchy), 
but this takes you to a landing page where you can see some details of the data 
and an actual citable (I think) reference to the data for a publication. There 
is a link to the data but the data has not yet been made public by the author 
or facility, but at least its (should be) there and will eventually be public. 
The responsibility is now on the facility for looking after  and making the 
data available.

This wouldn’t suit everyone, and also there is the issue of home sources, but 
tools are under development to make this easy. I could easily imagine that 
within the UK STFC would probably host something like this for non facility 
data (it is actually them who host Diamond data for us)…. Maybe at a nominal 
cost of course….

Long bit:
Something similar at Diamond, /dls/$Beamline_name/data/$Year/$proposal-$visit 
and permissions are set accordingly so only the people on the visit or the PI’s 
of the proposal can see the data therein. What happens within that directory is 
still pretty much the users choice at the moment. Though once the data is 
collected its read only and its all recorded in ISPyB (beamline database with 
web pages developed at ESRF and Diamond). You can also record details of the 
sample and link the data collections to it.

There is an EU funded initiative that I have make the IUCr DDDwg aware of in 
Europe called PanData (http://www.pan-data.eu/) which includes most of Europe’s 
X-ray and neutron sites. Under this initiative the facilities are attempting to 
standardise on authorisation, data formats, some software, access policies 
(making data public) data retention and cataloguing.

Here we’ve been a bit lucky to get ahead on this and we have been able to keep 
a copy of all our data off all beamlines, raw and processed on tape (that’s 
just under 200Tb and 53 million catalogued files so far, lots of data including 
processed data its not yet catalogued but is on tape). We are currently beta 
testing a web page to the data that is catalogued, so anyone who has collected 
data at diamond should be able to get it from https://icat.diamond.ac.uk. The 
data will probably be coming off tape so can take a while, also it’s a little 
bit clumsy as an interface but it will get better. This is the same technology 
as is being proposed for PanData facilities, but the backend of the actual data 
archive is the choice of each facility, ours is hosted in a tape robot by STFC 
at the moment.

This is by no means the only solution out there but DOI’s could help unify the 
solutions?

Alun
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Scientific Software Team Leader,  http://www.diamond.ac.uk/
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom Peat
Sent: 18 October 2011 23:29
To: ccp4bb
Subject: Re: [ccp4bb] IUCr committees, depositing images

If we are talking schemes, here is another one that we use that might be 
considered:

Date/person/project/barcode/well#/crystal#

At the Australian synchrotron, a directory is automatically made with the date, 
so that is our starting point.
We sometimes skip the person, but project-barcode-well are always there, as 
then it can correspond to our crystal database.
I imagine that most high throughput centres use barcodes, so barcodes and well 
numbers would be good things to have in the path.

Cheers, tom

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
mjvdwo...@netscape.net
Sent: Wednesday, 19 October 2011 6:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] IUCr committees, depositing images

Phoebe,

Just automate the archiving and come up with a reasonable scheme how to. Ours 
is that data sets are called:

userid_yearmonth_projectid_#

Userid is derived from the login into CrystalClear (oops, free advertizing), 
projectid is set by the PI (so she can remember 10 years from now what in the 
world these data are all about) and the users are asked (threatened) to call 
their data sets projectid_# (and not the ubiquitous test). We have a script 
that automatically archives everything away from our data collection computer 
into an archive - activated by an icon on the desktop - and it adds the userid 
and date to the filename. This has the nice added advantage that the data 
collection disk stays clean. This only breaks when we collect synchrotron data 
(which is all the time) because our synchrotron remote scientist who collects

[ccp4bb] Scientific software development post at Diamond Light Source, UK

[Alun Ashton]

Please see below details of a software development post available within the 
Scientific Software Team at Diamond. For full details please go to the web 
pages at:
http://www.diamond.ac.uk/Home/Jobs/Current/DIA0618-TH.html 

Job Title: Software Engineer  
Job Reference: DIA0618/TH  
Post Type: Full time / Permanent 
Division: Science 
Salary information: Circa £34k. Based on experience and qualifications; a 
higher salary may be available for an exceptionally experienced and qualified 
candidate. 
Application deadline: 10/06/2011 
Date of interviews: TBC  

We are looking for a high calibre software engineer to join our dynamic 
scientific software team. The team have the responsibility for the provision of 
advanced data evaluation, analysis and visualization software applications for 
both internal and external users of Diamond. These applications often exploit 
the very latest techniques to address the challenging requirements of a broad 
range of scientific disciplines including macromolecular crystallography 
through to nanostructures and materials science.

You will operate within the scientific software team of experienced software 
scientists and engineers and will work with our beamline scientists to identify 
and define requirements for data analysis and visualization applications and 
then ensure that they are implemented in a timely and effective way. It is 
important also to work with our data acquisition team to help optimize the 
whole scientific process at a Diamond beamline from data acquisition through to 
the experimenters leaving with high quality experimental results.

The work will also involve enhancing and supporting the core features of a 
scientific data analysis workbench project at Diamond and to work with 
collaborators on other similar facilities in the world.



Alun
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Scientific Software Team Leader,  http://www.diamond.ac.uk/
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.

[ccp4bb] Software development post at Diamond Light Source, UK

[Alun Ashton]

Please see below details of a software development post available at Diamond. 
For full details please go to the web pages at:

http://www.diamond.ac.uk/Home/Jobs/Current/DIA0608-TH.html 

Job Reference: DIA0608/TH  
Post Type: Full time / Permanent 
Division: Science 
Salary information: Circa £34k, dependent on assessment of previous relevant 
experience and qualifications. 
Application deadline: 31/03/2011 

We are looking for a high calibre software engineer to join our scientific 
software team. The team have the responsibility for the provision of advanced 
data evaluation, analysis and visualisation software applications for both 
internal and external users of Diamond. These applications often exploit the 
very latest techniques to address the challenging requirements of a broad range 
of scientific disciplines including macromolecular crystallography through to 
nanostructures and materials science.

You will operate within the scientific software team of experienced software 
scientists and engineers and will work with our beamline scientists to identify 
and define requirements for data analysis and visualisation applications and 
then ensure that they are implemented in a timely and effective way. It is 
important also to work with our data acquisition team to help optimise the 
whole scientific process at a Diamond beamline from data acquisition through to 
the experimenters leaving with high quality experimental results.

The work will also involve enhancing and supporting the core features of a 
scientific data analysis workbench project at Diamond and to work with 
collaborators on other similar facilities in the world.


Alun Ashton
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Scientific Software Team Leader,  http://www.diamond.ac.uk/
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.