The Hackathon Phenomenon

date-added: 2015-03-24 04:16:59 +0000 date-modified: 2015-03-24 04:16:59 +0000date-added: 2015-03-24 04:16:59 +0000 date-modified: 2015-03-24 04:16:59 +000

Digital Innovation: The Hackathon Phenomenon

date-added: 2015-03-24 04:16:59 +0000 date-modified: 2015-03-24 04:16:59 +0000date-added: 2015-03-24 04:16:59 +0000 date-modified: 2015-03-24 04:16:59 +0000This work was supported by the Arts and Humanities Research Council, CreativeWorks London Hub, grant AH/J005142/1, and the European Regional Development Fund, London Creative and Digital Fusion

Enriched biodiversity data as a resource and service

Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts

Hackathons: Why Co-Location?

This research was supported by the Arts and Humanities Research Council [grant Number AH/J005142/1].This research was supported by the Arts and Humanities Research Council [grant Number AH/J005142/1].This research was supported by the Arts and Humanities Research Council [grant Number AH/J005142/1].This research was supported by the Arts and Humanities Research Council [grant Number AH/J005142/1].In this position paper we outline and discuss co-location as a significant catalyst to knowledge exchange between participants for innovation at hackathon events. We draw on surveys and empirical evidence from participation in such events to conclude that the main incentives for participants are peer-to-peer learning and meaningful networking. We then consider why co-location provides an appropriate framework for these processes to occur, and emphasize the needs for future research in this area

Guidelines Towards Better Participation of Older Adults in Software Development Processes using a new SPIRAL Method and Participatory Approach

This paper presents a new method of engaging older participants in the process of application and IT solutions development for older adults for emerging IT and tech startups. A new method called SPIRAL (Support for Participant Involvement in Rapid and Agile software development Labs) is proposed which adds both sustainability and flexibility to the development process with older adults. This method is based on the participatory approach and user empowerment of older adults with the aid of a bootstrapped Living Lab concept and it goes beyond well established user-centered and empathic design. SPIRAL provides strategies for direct involvement of older participants in the software development processes from the very early stage to support the agile approach with rapid prototyping, in particular in new and emerging startup environments with limited capabilities, including time, team and resources

GMOD for Evolutionary Biology

The Generic Model Organism Database (GMOD, "http://gmod.org":http://gmod.org) project provides interoperable, open source software tools for managing, visualizing and annotating biological data. GMOD is also a community of people addressing common challenges with biological data. Some well known software in GMOD includes GBrowse and JBrowse for genome browsing, Apollo for genome annotation, Chado for managing data, CMap for comparative map viewing, Galaxy for workflow creation and persistence, and BioMart for warehousing biological data.

This talk will focus on three areas of particular interest to iEvoBio participants. 
1) GBrowse_syn comparative genomics viewer
2) Natural Diversity Module of the Chado database schema
3) GMOD evolutionary biology hackathon 

The GBrowse_syn comparative genomics viewer displays synteny between a reference and any number of related species. It shows inversions, duplications, and indels, and can show synteny across non-contiguous regions. It is built on the widely used GBrowse genome viewer. The Natural Diversity Module is an extension to GMOD’s Chado database schema to enable Chado to support natural diversity, population genomics, individuals, breeding, phenotypes and geolocation information. This module is the first extension to Chado to be designed by the community, rather than at one institution. We will close by soliciting nominations and ideas for a GMOD Evolutionary Biology Hackathon. This hackathon will be held November 8-12, at NESCent, which is sponsoring the event. There will be an open call for participation in August.
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