Halfway there!

We’ve seen the launch of the Leeds General Cemetery Company resources in November, a new catalogue for the Hey family archive material, and have so far digitised thousands of pages of manuscript volumes. It’s been an exciting and busy first 15 months!

There’s still lots more to do, and cataloguing is continuing. This week I’ve been preparing a new catalogue for the Bragg Family Collection (ref no: MS 81). A small collection of items with great significance, it centres on a notebook kept by Sir William Henry Bragg and his son, Sir (William) Lawrence Bragg.

Both of the Bragg’s were physicists; William Henry Bragg was Cavendish Professor of Physics here at the University of Leeds between 1909 and 1915. In the summer of 1913, father and son joined forces in Leeds to carry out experiments on the structure of crystals, using an X-ray spectrometer designed by William Henry Bragg. The notebook records the results of their experiments.

L0059138 Bragg X-ray spectrometer
Bragg X-ray spectrometer, England, 1910-26. Credit: Science Museum London, Wellcome Images. Copyright: work available under Creative Commons Attribution only licence CC BY 4.0 http://creativecommons.org/licenses/by/4.0/

Their pioneering research in establishing the nature of X-ray spectra and the principles of crystal analysis was recognised with the award of a joint Nobel Prize for Physics in 1915. Their work formed the basis of X-ray crystallography as a field of research – which laid the foundations for some hugely significant discoveries, such as the DNA double-helix in 1953, and the structures of haemoglobin and insulin.

The notebook was presented to the University by Lawrence Bragg on 20th June 1945, at a ceremony to unveil a tablet to commemorate their work. The tablet is displayed on the wall at the entrance to the Brotherton Library.

A digital copy of the notebook is available on the catalogue entry, and an online resource providing a more in-depth history of the Bragg’s work and analysis of the notebook can be found on our website.

Sources: Talal Debs, ‘Bragg, Sir William Henry (1862-1942)’,Oxford Dictionary of National Biography, Oxford University Press, 2004; online edn, Jan 2011 [http://www.oxforddnb.com/view/article/32031, accessed 21 Feb 2017]

University of Leeds website, News, ‘Plaque marks birthplace of X-ray crystallography’, 5 July 2013, https://www.leeds.ac.uk/news/article/3417/plaque_marks_birthplace_of_x-ray_crystallography [accessed 21 Feb 2017]


Preservation and Research Data files – ASCII

Let’s start with the plain text files.
In her blog posts Jenny Mitcham described the range of files appearing in the York repository, the use of available tools to identify these files, and the process of registering a file format with the National Archive in PRONOM. What have we got in our digital archive? , My first file format signature. The original post describing the data profiling at York is “Research data – what does it *really* look like?”

At Leeds we see a similar mix of file formats though perhaps with more arising from scientific instruments and software. Such file formats are sometimes recognised by the tools though often not. For those that are binary the registration process Jenny describes can be applied. What about the ACSII or text/plain files?

An example: At Leeds we make extensive use of a finite element software package called Abaqus (https://www.3ds.com/products-services/simulia/products/abaqus/) produced by Dassault Systemes. Have a look at one of our very earliest datasets and the sample Abaqus input file.
(Segmentation_model_S1a.inp in Hua, Xijin and Jones, Alison (2015) Parameterised contact model of pelvic bone and cartilage: development data set. University of Leeds. [Dataset] https://doi.org/10.5518/3).

Extracts from file Segmentation_model_S1a.inp

Header with start of section that defines the geometry


(then 200000 more Node lines)

Material properties and boundary conditions


(lots more lines of settings and processing commands)

Final step in the processing


Such files have a .inp file extension and can be created through one of the Abaqus suite of tools or manually using a text editor. The file header (lines starting with ** %) is produced by the Abaqus tools but is not processed and may not be present if the file is edited or created manually. The file contains some initial keyword based lines that set up the task, a large section that defines the mesh over the geometry, a series of keyword based commands that define material, boundary, and contact conditions then a keyword based section that defines the analysis itself. In the use of a structure with a controlled vocabulary and parameters and values it is much like a LaTeX or HTML or XML file.

The preservation tools correctly identified the file as mime-type text/plain. So human readable and no doubt understandable to a scientist in that field. So to some extent it can already be regarded as “preserved”. There are software vendor manuals that define the keywords and commands. With knowledge of finite element analysis, the input file, and the manuals a scientist in this discipline could reproduce the analysis whether or not they had a copy of the Abaqus software. Can we regard it as “even more preserved”?

If we do regard files in this format as “preserved” would it be reasonable to register the format in PRONOM even though we won’t be able to provide a signature – as has been done for .py (Python script) and a number of other formats?

If so should we work with the software vendors to create and maintain these registrations? Has this approach to preservation been explored before?

I have just started exploring digital preservation with Dassault Systemes. More to follow.

Branwell Brontë transcribed

2017 is 200th anniversary of Branwell Brontë’s birth. To mark this occasion, Special Collections has made digitial transcripts of letters written by Branwell available online in a new resource.

Branwell was the younger brother of the Brontë sisters. He is seen today as a tragic figure, whose life was marred by alcoholism, debt and longing for a married woman. Much of what we know about Branwell comes from letters written by the Brontës themselves. Many of the letters written by Branwell Brontë in the final years of his life are now part of Special Collections Brontë Family Manuscripts Collection. We have 24 letters in total, written by Brontë between 1842 and 1846.

Brontë wrote the majority of these letters after his dismissal from Thorp Green in July 1845. He had worked there as a tutor for the Robinsons, and was dismissed over a supposed affair with Mrs Robinson. The letters show that Brontë was very much in love with Mrs Robinson, and distraught at the end of their liaison. The letters also highlight Brontë’s ongoing mental health problems and alcoholism.

Many of the letters are illustrated, with sketches giving clues to Brontë’s state of mind at the time. These range from a sketch of a woman crying titled ‘Our Lady of Greif‘, to a self-portrait with a noose around his neck.

With the help of digital volunteers Special Collections crowd sourced transcriptions of Brontë’s letters in 2016.  The volunteers used Transcription Desk software to carefully transcribe each letter, including any misspellings or deletions.

The transcriptions are now available to read online, alongside images of each letter. Visitors to the webpage can also download Text Encoding Initiative standard XML transcriptions which provide even more detail on each letter.

The online letters provide a brilliant opportunity to gain intimate insight into the personal life of one of the literary world’s most troubled characters.



Chinese cookery in our collections

The annual Lantern Festival is one of the highlights of the Chinese calendar with feasting and celebrations.  We’re taking the opportunity to look at Chinese cookery books in our Cookery Collection.

 On 11th February it was Yuanxiao Festival known as the Lantern Festival. Traditionally people release ‘tiandeng’ — sky lanterns, view decorated lanterns through the night, attend dancing and singing performances and eat ‘yuanxiao’ or ‘tangyuan’.  It is the first full moon of the New Year, the day representing completion, perfection and a good day.  It marks the last day of the Lunar Chinese New Year.

Just like China’s other traditional holidays, the Lantern Festival has its own special dish – ‘yuanxiao’, or sweet dumpling soup. Amongst our Cookery Collection can be found the book ‘Zhongguo xiao chi‘ (1981).  An image from the book is shown. Page 77 informs us that: yuanxiao, also called ‘yuanzi’, ‘tangyuan’or ‘tuanzi’, existed during the Kaiyuan period (713-741 AD) of the Tang Dynasty, and: “家制米圆相饷,即呼之为元宵” which can be translated as: the rice ball made at home for a treat is called yuanxiao.

The filling is usually composed of different kinds of fruit kernels and sugar. Although the sweet dumplings differ in name and recipe from the North and South, they are always made with glutinous rice flour for the outside. The sweet dumplings are rounded and white, as this represents the moon on the night, and the wish and anticipation of family unity.  The name ‘tangyuan’ is more common in the South while the older name ‘yuanxiao’ is used in the North.

The Chinese lunar calendar has twenty four terms.  ‘The festive food of China‘ (1991) features special meals prepared and eaten to celebrate the different terms.  ‘China’s food: A photographic journey‘ (1986) formerly belonged to the food journalist Michael Bateman.  It is part of our extensive printed Bateman Collection.  The book is packed with stunning images of Chinese food.  Some photographs show the beauty of raw ingredients such as vegetables and grains.  They include intricate carvings of vegetables and fruit suitable for a grand banquet.

MOOC over

Well I passed…but my noble intention was to post every week about the course content, which I only managed for weeks one and two with a half-finished post languishing for week 3 ‘ Working with data’. Instead and in lieu of paying Coursera for a course certificate, I’ll just leave this here as proof of completion and try to pick out a few highlights below and how they relate to our service here at Leeds:


In my defence, this course was obviously an adjunct to my day job and though the content was good, I was disappointed by the lack of community, with very little activity on the course forums such that I gained little from the MOOC format than just working through the self-paced MANTRA course. Inevitably, also, this course was necessarily generic and one of the big challenges of RDM education I think is applying the theoretical principles to specific disciplines – indeed this is common feedback from the Research Data Management Essentials training we deliver at Leeds (I’ve just signed up for Data Management for Clinical Research from Vanderbilt University which started this week and which might inform our engagement with the Faculty of Medicine and Health).
Probably the main lesson I’ve learned, from the day job and reinforced by this course, is that each aspect of RDM is related to all the others which really drives home the importance of good data management planning.
Week 3: Working with Data 
Good file management in research is so obvious that a lot of researchers don’t give it proper consideration (citation needed) and it’s important to adopt conventions for directory structure, folder naming, file naming and versioning files, especially where files will be shared across a research team or with project partners. For University of Leeds guidance see https://library.leeds.ac.uk/research-data-organisation.
Storage, backup and data security is also crucial during the live stage of a project and we spend a lot of time poring over data management plans, advising researchers of institutional best practice. A challenge here is the sheer number of relevant institutional policies and we are working on a tool that helps to navigate these issues under the rubric ‘Safe Data Sharing Essentials’
File formats and transformations – Given the sheer number of proprietary file formats this is a major consideration for potential data reuse and for long term archiving and RDL recommends that wherever possible data should be saved in an open, non-proprietary, format. Of course this is not always possible and in a large, research intensive University there will always be specialist software outputting more or less exotic files and we must make informed decisions around reuse and preservation.
The UK Data Archive provides a table of optimal data formats but it is pragmatic rather than comprehensive and there is PRONOM, the technical registry from the National Archives, more comprehensive but less user-friendly.
We have been thinking about developing a resource to help inform these decisions, perhaps based on local file formats – a good idea from the University of Edinburgh that we might borrow is their File Format Registry Wiki.
I’m also looking forward to this upcoming webinar from the Open Preservation Forum on 27th February, Managing the Research Data Challenge.
Week 4: Sharing Data 
The clue is in the title that we also anticipate our ‘Safe Data Sharing Essentials’ toolkit will enable, well, safer sharing of data, especially (not only) qualitative data from human participants, through informed consent, ethical review and appropriate anonymisation for example.

As identified recently by David Kernohan “the point of article submission may be the first time a research has encountered the need to manage or share data” [Uses and abuses of journal data policies (part 1)] which can cause problems where there is inadequate consent for future reuse, for instance, and which may not have been fully considered at ethical review. We hope the toolkit will encourage data sharing, with safeguards where necessary (e.g. restricted access subject to an end user agreement.)

Week 5: Archiving Data
As per the earlier observation, archiving data cannot be taken in isolation and is probably the area in which I personally have the most to learn. We have begun to liaise with colleagues from Special Collections, looking at our respective data deposit workflows and it has been interesting to learn about their use of Bitcurator to analyse files. In addition to file formats/handling/preservation there are also synergies across our teams on policy and legal issues.
Special Collections have recently been awarded Accredited Archive Service status from the National Archives and we have also begun to think about working towards equivalent certification for our service, most likely the Data Seal of Approval.

Love in letters

With Valentine’s Day around the corner, we thought we’d highlight a letter on display in the Treasures of the Brotherton Gallery.

Now Valentine’s Day is approaching, we’re featuring a letter on show in the Treasures of the Brotherton Gallery.  This sheds light on the real life, tragic love story of one of Yorkshire’s most famous literary sisters.

On 27 January 1854, Charlotte Brontë wrote a letter from Cork, Ireland, describing her honeymoon with her husband, A. B. Nicholls. Arthur Bell Nicholls, one of her father, Patrick Brontë’s, curates first proposed to Charlotte in 1852. However, Charlotte’s father initially refused to approve the union on the grounds that a poor Irish pastor should never be bold enough to ask for the hand of his famous daughter.

Nicholls was redeployed to another parish for several months but he continued to see Charlotte in private.  He eventually persuaded her to marry him in June 1854, this time with Patrick’s permission.

Tragically, the couple only shared nine months of married life together. Charlotte died on 31 March, 1855, the cause of her death being listed as “phthisis” (tuberculosis). Many biographers now believe Charlotte died from the side effects of extreme morning sickness or from typhus.

So how did we get this incredible literary artefact? Thomas J. Wise, a collector, was responsible for the initial sale and distribution of the manuscript. Lord Brotherton was a fan of Brontëana, perhaps because of the family’s association with Yorkshire. Charlotte’s letter was acquired during the 1920s during the most prolific stage of Lord Brotherton’s book and manuscript buying.

The letter is currently on display in the Treasures of the Brotherton Gallery. We have also digitised the manuscript to make it accessible to everyone online.  It will be on display until late spring, and then we will be changing it for another item relating to Charlotte.

Open Research Leeds

Since it was set up in January 2012, mandated by Jisc as part of the Roadmap project, the Research Data Leeds @ResDataLeeds Twitter account has been somewhat underused with a grand total of 7 tweets between 2012 and 2015.

Latterly, however, we have been utilising the account a lot more, focusing on building a network, disseminating datasets and highlighting broader issues around RDM and scholarly communication so we are rebranding the account as Open Research Leeds @OpenResLeeds and will explicitly disseminate open access research papers from WRRO and associated datasets as primary research outputs. Please come and join our network!