Oxford Research Software Developers Network (Oxford RSDN)

On 05 May 2015 an email was circulated within the Digital Humanities at Oxford (University) calling colleagues that were working as research software (including data) developers. The idea was to keep in touch, share experiences and learn from each other; as well finding similar roles when contracts end (as University of Oxford works a lot with fixed-term contracts).

Part of the email from :

The Oxford e-Research Centre, Computer Science and the Digital Humanities are working to set up a University-wide network of “Research Software Developers” (RSDs): those who combine expertise in programming with an intricate understanding of research, and support the work of researchers in developing the (usually bespoke) software that is fundamental to so much of modern research. Many such people are employed across the University, but are not always well supported by cross-university structures. As a result they are often isolated and difficult to retain within the University. We are thus looking to connect these individuals in order to share expertise, provide appropriate advanced training, and facilitate re-employment with the University, hence optimising the use of their skills to enhance the University’s research.

A central support for the network will be a register of RSDs and their expertise, combined with a community forum and virtual employment exchange. Otherwise what the network does will be largely up to the members, but our ideas include regular meetings with talks from members or external speakers on new technologies, techniques they’ve found useful, case studies of how particular projects were tackled, and the like. We could run training sessions and hackathons to learn new tools/languages, or address common problems. There could also be research talks on relevant topics that have the potential to be transferred into RSE work.

After a short survey and a mail-list formed the first kick-off meeting happened on 8th June 2015. I’ve participate on this meeting (as a team member of the BDLSS) and below are some of my notes of the event… The people that had their names down (possibly starting it all) were:

  • Jonathan Cooper, Computer Science
  • David Robey, Oxford e-Research Centre & Digital Humanities
  • Wes Armour, Oxford e-Research Centre
  • Charles Crowther, Classics
  • Michael Davis, Bodleian Libraries

Jonathan Cooper started the discussion and presented a few ideas, based on the survey… Main focus was to get:

  • Frequency, location and time of day for regular meetings.
  • Content of the meetings, particularly for Michaelmas Term.
    • Summarise all the suggestions made through our survey.
  • Our proposal is to have short monthly meetings focused on lightning talks from members, as well as occasional longer events such as training courses or hackathons.

Create a representative body to:

  • facilitate find people and posts
  • lobby for recognition (role, pay, career)

Survey appointed these main interests:

  • sharing
  • networking
  • training
  • career development

Types of meetings we (RSDN) can do:

  • lightening talks
  • discussions
  • training courses
  • longer talks/presentations
  • hackathons
  • facilitating

In terms of content, we can focus on:

  • groups
  • services
  • material
  • courses

After a few discussions, the steps forward seemed to settle on:

  • monthly meetings (about 1-2hs)
  • lightening talks
  • discussion
  • and occasionally longer events.

A few points were made about the importance of having a profile within the network, to allow discoverability (even if you don’t have a whole CV there), but have basic information about the person and other links to your other profiles online (LinkedIn, Github accounts, etc.)

“As a group, it is easier to make a case for supporting this group in higher levels and allow hiring, collaboration, etc.”

An interest for a meeting on the summer time was raised, we’ll await more information via the mail list.

On 25/06/2015 a Slack account was created, which you can join at https://rsdn.slack.com/signup, and as long as you have a domain email listed you can participate.

The initial website for the Research Software Developers Network (Oxford RSDN) is at: http://rsdn.oerc.ox.ac.uk/

ICTF 2012


Raspberry Pi

by Daniel Bates


WHAT: It is a credit-card sized computer, it can connects to a mouse, keyboard, tv or monitor, power plug (you can use from your own mobile if you have a micro connector) and it has the following structure:

You can buy for $25 (without ethernet port) or $35 and despite they do have a backlog, on the conference was announced that it will clear in about a month or two. The demonstration of programming was OK, but the ‘media centre’ similar to X-box was really good. It is without doubt that has great potential for a simple use or for more interesting computing purposes. If you think about giving a presentation somewhere and you don’t want to carry your 1.5kg laptop you can consider carrying a ‘credit card’ and just plug into a screen/mouse/keyboard on the presentation venue. Impressive!

You can get many of your answers if you go to the Raspberry Pi FAQ page.

On the ‘designing a box’ for it, I just couldn’t resist to this Lego kit. Will be definitely getting one soon! (first need to order my R.Pi in UK can be bought from Farnell or RS)


Cisco and London 2012

by Ian Foddering

The London 2012 Olympic and Paralympic Games aim to be the most connected games to date.

Security, reliability and performance of the network infrastructure will be critical, with stability taking precedence over creativity. London 2012 is not about doing anything Cisco has not done before. Rather, it is all about doing what we do, but doing it better than ever.

Cisco are supplying the routing, switching, firewall and IP telephony to approximately 100 venues across the UK including:

  • 80,000 connections
  • 94 Locations
  • 2,220 Switches
  • 1800 WAPs
  • 7000 Cable TV sockets
  • 16,500 IP Phones
  • 65,000 active connections
  • 4 billion broadcast audience.
  • 6,500 Cisco WebEx licences
  • Show & Share plus MXE for “knowledge on Demand”

Interesting fact

I didn’t know, but London already hosted Olympic games twice, so this will be the third time! Years: 1908, 1948 and 2012!

Cisco is providing connectivity to the Olympic games, it is working with many partners to provide the service and it is expected to be the ‘most connected games ever’. Cloud technology is being used for first time. Even for the monitoring of construction sites and other Olympic-related business the partners/employees are using videos (Cisco call them ‘Show and Share’ so people can make a video of what is going on, hold meetings over internet or phone and discuss the progress of the work). Some of the technologies that are being used is the Cisco Webex (a free account, open to anyone allows 3 people per meeting, 250 MB storage, Standard video, Audio: VoIP (Internet), Share: Desktop, the premium account has more perks, check online if interested… However I wonder what is the real benefit of Webex compared with Skype…)

Some of the links shared:
Cisco.com/go/videos (which didn’t lead to anywhere… shame on the presenter! maybe try this one??? http://www.cisco.com/web/telepresence/video-conferencing.html

The presentation also mention Cisco and its relation with educational programs/partners. He mentioned the STEM initiative – Stem academy. One of the fronts will help people that might not have a chance to education and skill training (for financial/social reasons) to get the appropriate technological skills preparing them for the future. I like the way the word of “Legacy” appeared and how we should care/prepare to leave a good legacy and carry on our work into the future. The other front is to creates opportunities to inspire young people in Science, Technology, Engineering and Mathematics (STEM).

The presenter also mentioned the National Virtual Incubators and the BIG awards (just now I discovered that BIG stands for British Innovation Gateway! :P)


New digital initiatives at the Bodleian

by Michael Popham

Mike showed the DAMS structure, with emphasis on the preservation section. He showed a few screenshots of projects going on at the BDLSS, such as the Digital Images (Blockbooks), Digital.Bod, ORA (and explained what it is about). Mentioned the BEAM (futureARCH blog) – relating to the preservation theme/discussion; mentioined EMLO and showed a visualisation done with a 50-year-window to demonstrate the letters sent and received at that specific time. Mike also mentioned the scanning process and the workflow changing to BDLSS, making it more dynamic and fast. He showed a few other project screenshots such as Oxford google books, What’s the score? (the crowdsourcing part), mentioned that Bodleian also have an app for the Treasures of Bodleian (how come I just discovered this on the presentation???), the Queen Victoria project. We had questions about editorial on whatsthescore project (how to merge/combine/edit information coming from Zooniverse and how reliable that information is) and someone asked about the image kits/technologies used at the BDLSS.


Mobile Oxford

by Tim Fernando

OUCS will be replacing some structure for the Status.ox using Nagios and other kits (so if Nexus goes down status.ox doesn’t :)). Also replacing Events.ox, they are offering now Telecoms self-service (voicemail over web).

MobileOxford beginning: python, django, postgris; then went open source with Molly project.

Their process: Continuous deployment: commit (github), Jenkins (continuous integration), Fabric (deployment control, also see this blog for some info), Sentry (exception tracking), Puppet (helps system administrators manage infrastructure throughout its lifecycle), Pingdom (uptime monitoring)
elasticsearch (It is an Open Source – Apache 2, Distributed, RESTful, Search Engine built on top of Apache Lucene. Would this be better than Solr???)


Mobile Oxford website


Delivering Agile projects – Sprints, Scrums and Burndowns…

by Sara Passmore

She mentioned the Manifesto, which states:

We are uncovering better ways of developing software by doing it and helping others do it. Through this work we have come to value:

Individuals and interactions over processes and tools
Working software over comprehensive documentation
Customer collaboration over contract negotiation
Responding to change over following a plan

That is, while there is value in the items on
the right, we value the items on the left more.

Check names and other things at the Agile Manifesto site.

Sara has a DSDM training, which is similar to prince2 apparently. The important things that she said we could keep our minds to be able to deliver Agile projects are:

  • Fix time and cost, flex features (instead of the fixing features and flex cost and time). Contingency becomes the ‘nice to have’ features (instead of money or time for development). DSDM method uses numbering system instead of Moscow (must have, should have….)
  • “Built incrementally but on strong foundations”. Use Sprints.
  • Communication (stand up meetings, lean documentation – email and list of decisions).
  • Test early and continuously. Try creating unit-tests
  • Demonstrate control, empower team this will enable creativity


Her suggestions were to use timeboxes or sprints plus burn down chart, developers define task time! (points or hours, check cards -poker issue, until agreement is reached). Try to demo the system with user as the project goes along so they can be involved and also give feedback on how the features should behave according to their expectations. She also mentioned a possibility to give access to users to the development site so they can see the project on early stages (communication and someone filtering complaints or features suggestions could be needed for development)


Go live early with minimum set of features.


She recommended Keith Richard’s book Agile project management: running PRINCE2 projects with DSDM Atern. And he has a consultancy/training site.


She mentioned Microsoft dynamics (don’t remember why now, sorry… maybe they offer Agile support/services?)


Experiments into Biology – Technology Interaction

by Kevin Warwick

In this presentation a practical look is taken at how the use of implant and electrode technology can be employed to create biological brains for robots, to enable human enhancement and to diminish the effects of certain neural illnesses. In all cases the end result is to increase the range of abilities of the recipients. An indication is given of a number of areas in which such technology has already had a profound effect, a key element being the need for a clear interface linking a biological brain directly with computer technology.

The emphasis is clearly placed on experimental scientific studies that have been and are being undertaken and reported on. The area of focus is notably the need for a biological/technological connection, where a link is made directly with the cerebral cortex and/or nervous system. The presentation will consider the future in which robots have biological, or part-biological, brains and in which neural implants link the human nervous system bi-directionally with technology and the internet.

This presentation was so good and interesting that was really hard to take notes… he demonstrated a few implants that he had installed on himself, (Class II implants (RFID) arm and nervous system), mentioned Sensory substitution – where some students had implants on their fingertips (to allow detection of nearby objects by their vibration(?)) and a sensor in one student’s tongue.


Some great experiments:

  • Bi-direction communication: he was able to demonstrate (play video where he had) control of a robotic had over the internet (he was in different country where the robot hand was).
  • Implant on his arm and his wife’s arm and while blindfolded he could detect when his wife opened/closed the hand
  • Deep brain stimulation amazing stimulation of brain, on Parkinson’s disease, epilepsy, etc. The presenter showed a video of a person with Parkinson’s disease and the amazing benefit of an implant straight into the patient’s brain, stopping the tremors and allowing him to not only move hands and arms in a normal way, the patient was able to walk (and spin) at this own will, without assistance (as he has to, without the activated implant)
  • In USA patients with diabetes and epilepsy had implant in their hands to know exactly which medication they are using in case of an accident/event, where the hospital/ER would scan and detect the doses faster and accurately (apparently this is now regulated).
  • Robot with live brain cells learning to turn if wall is detected by sensor.


And Kevin Warwick also mentioned about “Enhancements”: memory, communication, senses, multi-dimensional thinking, extending the body, in build machine, etc. (for the creation of the super-human)


Kevin Warwick’s website: http://www.kevinwarwick.com/
And there are some videos of/about Kevin on youtube.


ICTF 2011

We had a great conference this year. In my opinion the topics were more relevant and presentations had more quality. To know who is who check: http://www.ictf.ox.ac.uk/conference/2011/whos-who.html

Please note that PDFs of the workshops can now be found here: http://www.ictf.ox.ac.uk/conference/2011/workshops.html

An Introduction to Biometrics by Julian Ashbourn

He gave some examples to illustrate ‘history’:
Egyptians – had a way to identify people using marks on forehead, etc
Galton Eugenics
Henry Goddard – Feeble-Mindedness
Juan Vucetich – fingerprint system based upon Galton’s ideas. First positive identification – Francisca Rojas – adopted by police – Galton-Henry system adopted by Scotland Yard

So, biometrics is not new idea…. what changed through time was the use of computers/technology to allow automation.

How does it work

  • define what we want to measure/match
  • extract features/biometric reference
  • statement of ‘likeness’

Two moments:
1. Registration – capture sample, extract features, create reference/biometric code (hash)
2. Live operation – capture sample, extract freatures, create code, retrieve stored code and compare!!!
– problems with accuracy and false positives – what comes to my mind is the case of Shirley McKie, for example (false positive, or better, a lack of proper judgment from the specialists involved)

The use of “User Psychology Index” to compare theoretical performance vs real performance. You can check some sample images from a software that does that.

Biometric matching is not an exact science…

Where to use? everything? security? convenience only?
Who the biometrics belongs to? Americans say it theirs, a person say that is theirs. So depends who holds it/the information, who will decide how is going to be used? Should a biometric be covertly? (here he gave an example of people watching a big screen and the screen scanned the ‘biometrics’ and started to show information on screen according to analysis on the public / face recognition (male/female, age, etc).)

Because it is biometric doesn’t mean that is correct.

Enrollment procedure very important. Establishin and identity, template quality (if the quality is bad, you can have bad data), user instruction, etc.
Be extra careful about exception handling; repudiation; and use of biometric forensics.

Ideas, new frontiers…

  • Biometrics in the cloud – (my personal reaction: “aaaaaaaaaaahhhh”)
  • Federated identities – implications for the registration process, who owns them? who services them? WHO MAINTAINS THE DIRECTORY OF BIOMETRICS?
  • Aligntment with profiles, privileges, location, device and other factors.
  • Virtualised environments and identity measures

Brave new world
Do we want the William Shakespeare version of it?

O, wonder!
How many goodly creatures are there here!
How beauteous mankind is! O brave new world,
That has such people in’t!
The Tempest (V, i)

OR these other verions:
Aldus Huxley, George Orewell, H.G. Wells

Final conclusion

Maybe is a good time to take a fresh look at what we might achieve with this technology.

  • Re-statement of relevance (where to use),
  • best practices around the systems integration,
  • clarity around privacy, ownership and data protection (on an international scale).
  • Clarity of purpose with respect to large scale public sector applications (and communication)

Book suggestion (same author): Guide to Biometrics for Large-Scale Systems – ISBN 978-0-85729-466-1

The Python Scripting Language by Bruce Beckles (e-Science specialist)

Did some interviews to academics/students/staff to identify what they need in computing support.
Answers: basic programming skills, easy access to libraries (not reinvent the wheel), lack of time (scientists, not programmers), return of investment.
Then, repeated the interview to social science and answers were the same/similar.

Why python?

  • good first language – match basic programming skills
  • loads of libraries available
  • ‘instant gratification’ because is interpreted
  • strict about syntax
  • object oriented
  • does its own garbage collection
  • dynamically typed/strongly typed

Common ‘academic’ libraries:
NumPy – numerical python
SciPy – scientific python – scipy.org/Topical_Software

There is a Python Package Index – http://pypi.python.org/pypi – that could help in finding the package you might need.


the capacity of being everywhere or in all places at the same time

Python everywhere: OS, types of application, disciplines, people

Alternative Implementations

  • CPython – bytecode interpreter
  • IronPython .net
  • Jython – Java
  • Stackless – Branch of CPython supporting microthreads

Where used?
Many places/projects, a few examples:

  • Eve Online – multiplayer online game, written in stackless python
  • Web apps – Django, turbogears, Zope/Plone,
  • Graphical applications in Linux are written in Python
  • Glade – gui builder written in Python, can be use to create GUI
  • Robots:PyVISA and PySerial
  • Embedded systems — mesh network
  • Written in Python:
    • Gutenkarte – book catalog
    • PyArchint – excavatioon management tool
    • Pleiades – cartographic framework

Integration/interfacing with existing code:
c, c++ > swig > python
fortran > f2py > python
java > jython > python
.net > ironPython > python

Python 2 (still supported for about 3-4 years), slowly the most common libraries are being converted to Python 3

Suggested links:
Python, an introduction to Computer Science – http://mcsp.wartburg.edu/zelle/python
Cambridge Computing Service Python course

Challenge for Computer SVCS in HE by Tom Mortimer

UCISA – Conferences, training sessions, lobbing in all UK universities

Top concerns:
1 – ongoing funding and sustainable resourcing of IT
2 – delivering services under sever financial constraint (new concern compared to 2008)
3 – providing a quality, resilent service (structure of service)
4 – IT strategy and planning
5 = business systems to support the institution
5 = organisational change and process improvement
7 – IT/IS service quality (delivery of the service)
8 = benchmarking, costing and value for money (new concern compared to 2008) – 2011 meeting – Know your numbers
8 = mobile computing, anytime, anywhere computing, home working (new concern compared to 2008) 2011 meeting done by Paul Golding
10 = cloud, managed services and alternative service delivery models (new concern compared to 2008)
10 = use of technology in teaching
12 – governance of IT

Concerns that are ‘out’: environmental and energy and data centres (feel that these concerns were ‘dealt with’)

Iceberg example (12% above water, 88% below)

How IT spend money: 5-15% transform, 5-15% grow, 70-90% run the business
IT expenditure – driven by business needs and funding pressures

Ideally increase percentages of transformation and growth to up to 40% and reduce the running of the business to 60% through resources and funding.

Multi-platform Mobile Apps by Greg Jennings (IT manager – Hertford College)

Started with DVDs for things about Hertford. Film, sound track with orchestra, 20000 cds over the years….
But to reduce costs and look ‘in the loop of technology’ they decided to invest in mobile apps. Starting with iOS then add one another platform per year.

Phonegap – framework for making apps. Don’t need to relarn Object C, can design for many platforms (symbian, iOS, #Blackberry, etc…)
What phonegaps gives you: accelerometer, geolocation, etc…

What you will need: html + css + phonegap + device + SDK
Starting from iOS/android – they limited their project to 50hs development if it was to be longer than that they would scratch the idea.
Phonegap, jQTouch – free

How to start
Design – keep it simple, design on paper first (useful article, not included on the ICTF, if you like wireframing, I highly recommend Balsamiq mockups)
XCode, – (xcode3 is quite nicer, but xcode4 is the way to go now…), Phonegap, JQTouch (get the whole bundle except the demos, they are too big)

Basic index.html

hello world, you can go here or there
this is here
this is there

Images are usually PNGa

PhoneGap Build – compress files into a zip and upload it don’t need to use multiple compiles

Testing – repeat the process many times, get tested on simulator, get tested on devices, etc

Publishing – screenshots, icons, descriptions, android self sign or tun off trusted sources – apple requires a registered CA or development device (ad hoc, jail broken, b2b) – android market updates happen synchronously – iTunes take 2 days but 14 days for ‘review’.

The results – iTune connect is poor and is yesterday’s info – iTunes connect is ok, android market is great android app andlytics is great app

Json – why should you use it? it is small/compact/great – why not xml? because doesn’t scale well, too much info you don’t need to know.

Building a search – mysql back end, php ‘fuzzy’ query page, separate page lookup.html within the app for ease of writing – what we wanted it to do: either retain user details or do a look up of anyone’s details. (this part I missed a bit, so it may clarify when I get an update with the presenter’s slides)


Green Open data & sustainability by Alex Dutton and Howard Noble

Main idea: check how much saving happens with people turning off their pc before going home. Also, making this data available so people get aware of it.

Meter data is open at Oxford

Problem with efergy – smart metering – might help in the begining but once you don’t have more reduction people will get bored and start to consume more.

Ways of presenting the information to people:

  • Graph A-G rating (like the refrigerator scale)
  • Are we saving energy? NO, 2.7% more than UK.
  • tidystreet.org – graph on street
  • Graph with the polar bear sad – not very good for some people
  • Energy dashboard – showing in reception

I urge developers to use data.ox.ac.uk to represent electricity as a public good, i.e. help others understand how private consuption has public ramifications. Help reduce the ignorance that propelling us to a tragedy of the commons and/or social injustices with respect to electricity, clean water, air quality, natural gas, nuclear waste, fish stocks…
Please get creative with the University electricity meter readins and help us upload more data sets.

More widgets on website – “how we are doing”
Tags/barcodes on bins to weight how much is reclyclable or not

Apple Technology Update by Stuart Anderson

OS X Lion is the new release (the new big cat) has 250+ new features as:

  • muti-touch gestures
  • full-screen apps
  • mission control
  • mac app store
  • launchpad
  • resume and auto save
  • versions
  • mail with ‘conversations’ (which looks a lot like the google mail already
  • server

Voices downloaded as needed; no printer drivers, just download when necessary; accessibility inherited – if you have a mac desktop then you can connect an iphone, ipad to it and it will inherit your accessibility features (hi-contrast, or color scheme for example).

  • File vault – encrypt your home folder
  • iCal has colouring code for slots that are too busy (a way to show you that you shouldn’t add any more opinion)
  • Launchpad – applications organised by category
  • Search – faster
  • Networking – you can wake up a specific drive for backup without having to wake up all drives automatically, they support DFS now
  • Preview – can open word documents in Preview
  • Privacy – location data, who can use
  • QuickTime Player – share directly to Flickr and Facebook
  • Resume – resume the whole state of the computer
  • Safari – loads of features, populating email
  • Screen Sharing – can see under the hood not only screen itself
  • Spotlight search – gives a preview while scrolling on the list
  • System – general system: can import everything from Windows machine, AppleID
  • Text – improving on the entering too
  • TextEdit – revert to other version (only the final version)???
  • Time machine – not always have to be online, back it up daily just syncronyse when you are online
  • Version – browse between versions of your document, nice interface
  • Resize from the corners (in Windows for ages, but now in Mac)
  • Multiple desktops (Linux has for ages)
  • Integrated Mac Store
  • AirDrop (friends around can receive documents without worrying about network configuration)
  • Mail Server 3 – beautifully design interface (finally)

iOS 5 200+ features

  • notification cente
  • newstand
  • reminder
  • twitter integrated
  • faster safari
  • reader – get the ‘clutter’ out of the way, just show content
  • photo – accessible from main
  • split keyboard to make it easier to type
  • share with the TV: show on tv what you are seeing on the iPad (you need an Apple TV for that)


  • content in all devices
  • 5GB free storage
  • itunes in the cloud
  • photo stream (+apple tv)
  • apps, books, documents and backup
  • contacts, calendar and mail (me.com)
  • iCloud API
  • available in full this autumn

Sense and Sendability – Novel Mobile Devices for the Future by Lyndsay Williams


My personal comment on this presentation: very amusing, this woman did LOADS, and some very creative things!!! Hard to describe in words… well, some of her inventions:

  • Camera to take pictures of room when a person crosses a door, the door frame gives a very different change in shadow: to aid people with memory problems.
  • SenseSurface – Knob to adjust volume on lcd screen but real 3d experience
  • Hand tracker for mobile phones
  • Detection of tremor of someone having epilepsy (hand sensor detector)
  • Thrill chip – record and replay skin sensations, touch, replay feeling with skin actuators like chill, heat, nerve stimulation – http://tinyurl.com/6eyvko9
  • Microsoft GyroTablet handheld computer with motion detection

Please have a look on her slide presentation – found on her website – it has links to youtube videos with demonstration of the technologies… http://girtonlabs.s3.amazonaws.com/GirtonLabsv260809a.pdf