Datascape

"Contemporary society is in the midst of the boundless generation and collection of data, data that is produced from almost any measurable act. Be it weather or transport data sets published by government agencies, or the individual and interpersonal data generated by our digital interactions; a server somewhere is collating. With the rise of this digital data phenomenon comes questions of comprehension, purpose, ownership and translation. Without mediation digital data is an immense abstract list of text and numbers and in this abstracted form data sets become detached from the circumstances of their creation. Artists and digital creatives are building works from these constantly evolving data sets to develop a discourse that investigates, appropriates, reveals and reflects upon the society and environment that generates this medium. Datascape presents a range of works that use data as building blocks to facilitate connections and understanding around a range of personal, social and worldly issues. The exhibition is concerned with creating an opportunity for experiential discovery through engaging with work from some of the world’s prominent creatives in this field of practice. Utilising three thematic lenses: Generative Currents, the Anti-Sublime and the Human Context, the works offer a variety of pathways to traverse the Datascape. Lubi Thomas and Rachael Parsons, QUT Creative Industries Precinct"

Proceedings of the Digital Cities 9 Workshop - Hackable Cities – From Subversive City Making to Systemic Change (Workshop) [Edited Proceedings]

The DC9 workshop takes place on June 27, 2015 in Limerick, Ireland and is titled “Hackable Cities: From Subversive City Making to Systemic Change”. The notion of “hacking” originates from the world of media technologies but is increasingly often being used for creative ideals and practices of city making. “City hacking” evokes more participatory, inclusive, decentralized, playful and subversive alternatives to often top-down ICT implementations in smart city making. However, these discourses about “hacking the city” are used ambiguously and are loaded with various ideological presumptions, which makes the term also problematic. For some “urban hacking” is about empowering citizens to organize around communal issues and perform aesthetic urban interventions. For others it raises questions about governance: what kind of “city hacks” should be encouraged or not, and who decides? Can city hacking be curated? For yet others, trendy participatory buzzwords like these are masquerades for deeply libertarian neoliberal values. Furthermore, a question is how “city hacking” may mature from the tactical level of smart and often playful interventions to the strategic level of enduring impact. The Digital Cities 9 workshop welcomes papers that explore the idea of “hackable city making” in constructive and critical ways.

Gentlemen Songsters

This project was initially envisaged as a compare and contrast proposition between two performances in music venues, a year apart, at the Melbourne Ukulele Festivals 2013 and 2014. The covert intermedial incorporation of scripted, theatrical elements into an ostensibly musical performance was the initial focus. However, the opportunity arose to continue the creative practice towards a performance outcome at the Queensland Cabaret Festival at the Brisbane Powerhouse in June of 2014. This expanded project was titled ‘Gentlemen Songsters’ and enabled a refinement and honing of the event beyond what was initially planned. In addition to the composition, recording and curation of original songs, this process involved two cycles of performance, videography, transcription, re-writing and re-performance. Led by this creative practice, the research investigated the potential for sonata and song cycle as influences on performance structure, in the creation and performance of Composed Theatre. This manifested as a theatricalisation of compositional processes. Performed by ‘Tyrone and Lesley’, performance personae of David Megarrity (lyricist/composer/performer/ukulele) and Samuel Vincent (composer, musician, performer), Gentlemen Songsters played at the Brisbane Powerhouse as part of its inaugural Queensland Cabaret Festival on June 13 2014

Straightforward data management at QUT

QUT Library Research Support has simplified and streamlined the process of research data management planning, storage, discovery and reuse through collaboration and the use of integrated and tailored online tools, and a simplification of the metadata schema. This poster presents the integrated data management services a QUT, including QUT’s Data Management Planning Tool, Research Data Finder, Spatial Data Finder and Software Finder, and information on the simplified Registry Interchange Format – Collections and Services (RIF-CS) Schema. The QUT Data Management Planning (DMP) Tool was built using the Digital Curation Centre’s DMP Online Tool and modified to QUT’s needs and policies. The tool allows researchers and Higher Degree Research students to plan how to handle research data throughout the active phase of their research. The plan is promoted as a ‘live’ document’ and researchers are encouraged to update it as required. The information entered into the plan can be made private or shared with supervisors, project members and external examiners. A plan is mandatory when requesting storage space on the QUT Research Data Storage Service. QUT’s Research Data Finder is integrated with QUT’s Academic Profiles and the Data Management Planning Tool to create a seamless data management process. This process aims to encourage the creation of high quality rich records which facilitate discovery and reuse of quality data. The Registry Interchange Format – Collections and Services (RIF-CS) Schema that is used in the QUT Research Data Finder was simplified to “RIF-CS lite” to reflect mandatory and optional metadata requirements. RIF-CS lite removed schema fields that were underused or extra to the needs of the users and system. This has reduced the amount of metadata fields required from users and made integration of systems a far more simple process where field content is easily shared across services making the process of collecting metadata as transparent as possible.

Distribution Revolution: Conversations about the Digital Future of Film and Television

Distribution Revolution is a collection of interviews with leading film and TV professionals concerning the many ways that digital delivery systems are transforming the entertainment business. These interviews provide lively insider accounts from studio executives, distribution professionals, and creative talent of the tumultuous transformation of film and TV in the digital era. The first section features interviews with top executives at major Hollywood studios, providing a window into the big-picture concerns of media conglomerates with respect to changing business models, revenue streams, and audience behaviors. The second focuses on innovative enterprises that are providing path-breaking models for new modes of content creation, curation, and distribution—creatively meshing the strategies and practices of Hollywood and Silicon Valley. And the final section offers insights from creative talent whose professional practices, compensation, and everyday working conditions have been transformed over the past ten years. Taken together, these interviews demonstrate that virtually every aspect of the film and television businesses is being affected by the digital distribution revolution, a revolution that has likely just begun. Interviewees include: • Gary Newman, Chairman, 20th Century Fox Television • Kelly Summers, Former Vice President, Global Business Development and New Media Strategy, Walt Disney Studios • Thomas Gewecke, Chief Digital Officer and Executive Vice President, Strategy and Business Development, Warner Bros. Entertainment • Ted Sarandos, Chief Content Officer, Netflix • Felicia D. Henderson, Writer-Producer, Soul Food, Gossip Girl • Dick Wolf, Executive Producer and Creator, Law & Order

Book Reviews: "Fashion Media: Past and Present"

The book Fashion Media: Past and Present is a timely insight into the historical relationship between fashion and media. Edited by Djurdja Bartlett (Senior Research Fellow at the London College of Fashion), Shaun Cole (Course Leader for the MA in the History and Culture of Fashion and MA Fashion Curation at the London College of Fashion) and Agnès Rocamora (Reader in Social and Cultural Studies at the London College of Fashion), Fashion Media offers a wide historical perspective on how painting, photography, film, television and the Internet have intersected with fashion. The book also provides a useful understanding of social and cultural key issues related to this synergy...

De Profundis (Theatre Soundtrack)

This creative work is an original soundtrack for the multimedia performance adaptation of Oscar Wilde’s De Profundis, led by David Fenton and Brian Lucas and produced by Metro Arts. Intermediality offers unique challenges to the composer creating towards live performance. Given the text-based nature of the piece, and the prevalence of screen content, music had a distinct role to play in supporting the intermedial performance environment. Drawing from Oscar Wilde’s own writings in the initial stages [“...richer cadences…more curious effects” “…the cry of Marysas” and the “deferred resolution of Chopin”] , the deliberately risky compositional process experimented with improvised location recordings and found sounds, random and fragmented assemblages of vintage recordings, rough methods and obsolete recording technology, and the sonic kinship of the hissing sibilances of the sea, theatrical applause and the crackle of antique recording devices (which had just been invented in Wilde’s time) worked into wefts of sound. As the soundtrack emerged, is was clearly resistant to ‘concepts’ imposed from the outside, and as the field of possibilities expanded and engaged in dialogue with the other elements of the performance (live and projected) certain pieces were selected by the director and curated into the emerging work. Thus leitmotifs emerged, rather than being imposed from the outset, with a particular through line holding: if it was too obviously like ‘music’, (which is usually used in theatre as emotional lubrication and narrative signpost) it didn’t work, and if it sounded like avant-garde sound-art, it was too grating and detracted from the primacy of the text. As a composer I worked this sweet spot inbetween these two poles as well as serving David Fenton’s curation: he determined which compositions to incorporate, reiterate and omit as part of the process of writing text, action and image and the compositional process responded with organic elaborations and variations on these selections. Musical resolution was mostly deferred until the closing stages of the performance. The soundtrack was present for the duration of the show, and Artshub reviewed the musical component thus: “...the score by David Megarrity is a refined, understated ambient scaffolding.” It premiered at the Visy Theatre, Brisbane Powerhouse, on 22 April 2015.

Remember or Revive: Alice Payne and the Gold Coast and Hinterland Historical Society

In this creative practice work, designer Alice Payne examines the history of twentieth century Queensland fashion icon Paula Stafford, and interprets her story into an illustrated narrative and textile print. Paula Stafford was a swimwear designer operating in the Gold Coast, Queensland Australia 1940s to 1980s, and is credited with bringing the bikini to Australia. This project was commissioned by The Fashion Archives as part of their series Remember or Revive, in which the curators partnered designers with museums to reinterpret historical costume for a contemporary fashion audience. To develop the project, Payne visited The Gold Coast and Hinterland Historical Society to view Paula Stafford’s swimwear, resortwear, photographs, newspaper articles, fabric swatches and other artefacts relating to Stafford’s practice. Through examining Stafford’s work and history, Payne developed a series of designs based on the story and the experience of viewing and handling the garments. Research statement Fashion history is often experienced via static museum displays of garments and photographs from the period, and this research examines other means through which the archive and the fashion museum collection may be reinterpreted and made fresh. It does this in two ways: first, the work interprets a story from fashion history for a contemporary audience. Second, the project illuminates the fashion design process by demonstrating how garments from the past may be reinterpreted to inspire contemporary textile prints. The Paula Stafford collection at The Gold Coast and Hinterland Historical Society has a number of garments and photographs on display, however these only show a partial picture of the richness of Stafford’s work and legacy. Undertaking a practice-led methodology, in the course of developing the work, Payne examined the archive in order to interpret Stafford’s contribution to Queensland fashion through photography, narrative, and illustration. The work contributes to research into historical fashion curation and interpretation. The work appeared in Issue 11, March 2014 of the The Fashion Archives, an online publication by fashion curators Nadia Buick and Madeline King. The Fashion Archives has received funding from Arts Queensland, State Library Queensland and Creative Partnerships Australia and has published over 200 articles and projects related to Queensland Style. The Fashion Archives is the first project to examine in depth Queensland fashion history. As Paula Stafford is one of Queensland’s most iconic designers, this project is significant in being the first to examine her legacy through creative practice. The Fashion Archives was established in 2013 and involvement is by invitation from the curators.

Using a botanic garden collection to test a bioclimatic vegetation scheme

Vegetation maps and bioclimatic zone classifications communicate the vegetation of an area and are used to explain how the environment regulates the occurrence of plants on large scales. Many practises and methods for dividing the world’s vegetation into smaller entities have been presented. Climatic parameters, floristic characteristics, or edaphic features have been relied upon as decisive factors, and plant species have been used as indicators for vegetation types or zones. Systems depicting vegetation patterns that mainly reflect climatic variation are termed ‘bioclimatic’ vegetation maps. Based on these it has been judged logical to deduce that plants moved between corresponding bioclimatic areas should thrive in the target location, whereas plants moved from a different zone should languish. This principle is routinely applied in forestry and horticulture but actual tests of the validity of bioclimatic maps in this sense seem scanty. In this study I tested the Finnish bioclimatic vegetation zone system (BZS). Relying on the plant collection of Helsinki University Botanic Garden’s Kumpula collection, which according to the BZS is situated at the northern limit of the hemiboreal zone, I aimed to test how the plants’ survival depends on their provenance. My expectation was that plants from the hemiboreal or southern boreal zones should do best in Kumpula, whereas plants from more southern and more northern zones should show progressively lower survival probabilities. I estimated probability of survival using collection database information of plant accessions of known wild origin grown in Kumpula since the mid 1990s, and logistic regression models. The total number of accessions I included in the analyses was 494. Because of problems with some accessions I chose to separately analyse a subset of the complete data, which included 379 accessions. I also analysed different growth forms separately in order to identify differences in probability of survival due to different life strategies. In most analyses accessions of temperate and hemiarctic origin showed lower survival probability than those originating from any of the boreal subzones, which among them exhibited rather evenly high probabilities. Exceptionally mild and wet winters during the study period may have killed off hemiarctic plants. Some winters may have been too harsh for temperate accessions. Trees behaved differently: they showed an almost steadily increasing survival probability from temperate to northern boreal origins. Various factors that could not be controlled for may have affected the results, some of which were difficult to interpret. This was the case in particular with herbs, for which the reliability of the analysis suffered because of difficulties in managing their curatorial data. In all, the results gave some support to the BZS, and especially its hierarchical zonation. However, I question the validity of the formulation of the hypothesis I tested since it may not be entirely justified by the BZS, which was designed for intercontinental comparison of vegetation zones, but not specifically for transcontinental provenance trials. I conclude that botanic gardens should pay due attention to information management and curational practices to ensure the widest possible applicability of their plant collections.

DoSA: Database of Structural Alignments

Protein structure alignment is a crucial step in protein structure-function analysis. Despite the advances in protein structure alignment algorithms, some of the local conformationally similar regions are mislabeled as structurally variable regions (SVRs). These regions are not well superimposed because of differences in their spatial orientations. The Database of Structural Alignments (DoSA) addresses this gap in identification of local structural similarities obscured in global protein structural alignments by realigning SVRs using an algorithm based on protein blocks. A set of protein blocks is a structural alphabet that abstracts protein structures into 16 unique local structural motifs. DoSA provides unique information about 159 780 conformationally similar and 56 140 conformationally dissimilar SVRs in 74 705 pairwise structural alignments of homologous proteins. The information provided on conformationally similar and dissimilar SVRs can be helpful to model loop regions. It is also conceivable that conformationally similar SVRs with conserved residues could potentially contribute toward functional integrity of homologues, and hence identifying such SVRs could be helpful in understanding the structural basis of protein function.

PLIC: protein-ligand interaction clusters

Most of the biological processes are governed through specific protein-ligand interactions. Discerning different components that contribute toward a favorable protein-ligand interaction could contribute significantly toward better understanding protein function, rationalizing drug design and obtaining design principles for protein engineering. The Protein Data Bank (PDB) currently hosts the structure of similar to 68 000 protein-ligand complexes. Although several databases exist that classify proteins according to sequence and structure, a mere handful of them annotate and classify protein-ligand interactions and provide information on different attributes of molecular recognition. In this study, an exhaustive comparison of all the biologically relevant ligand-binding sites (84 846 sites) has been conducted using PocketMatch: a rapid, parallel, in-house algorithm. PocketMatch quantifies the similarity between binding sites based on structural descriptors and residue attributes. A similarity network was constructed using binding sites whose PocketMatch scores exceeded a high similarity threshold (0.80). The binding site similarity network was clustered into discrete sets of similar sites using the Markov clustering (MCL) algorithm. Furthermore, various computational tools have been used to study different attributes of interactions within the individual clusters. The attributes can be roughly divided into (i) binding site characteristics including pocket shape, nature of residues and interaction profiles with different kinds of atomic probes, (ii) atomic contacts consisting of various types of polar, hydrophobic and aromatic contacts along with binding site water molecules that could play crucial roles in protein-ligand interactions and (iii) binding energetics involved in interactions derived from scoring functions developed for docking. For each ligand-binding site in each protein in the PDB, site similarity information, clusters they belong to and description of site attributes are provided as a relational database-protein-ligand interaction clusters (PLIC).

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

SInCRe-structural interactome computational resource for Mycobacterium tuberculosis

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein-protein and protein-small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein-protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host-pathogen protein-protein interactions. Together they provide prerequisites for identification of off-target binding.

Keeping Research Data Safe: a cost model and guidance for UK universities (KRDS1)

This study has investigated the medium to long term costs to Higher Education Institutions (HEIs) of the preservation of research data and developed guidance to HEFCE and institutions on these issues. It has provided an essential methodological foundation on research data costs for the forthcoming HEFCE-sponsored feasibility study for a UK Research Data Service.It will also assist HEIs and funding bodies wishing to establish strategies and TRAC costings for long-term data management and archiving. The rising tide of digital research data raises issues relating to access, curation and preservation for HEIs and within the UK a growing number of research funders are now implementing policies requiring researchers to submit data management, preservation or data sharing plans with their funding applications.