sciforge lightning talk at Collaborations Workshop 2015 (CW15)

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Collaborations Workshop 2015 (CW15) - interdisciplinary working and its relationship to software Oxford, March 25-27, 2015 http://www.software.ac.uk/cw15

Wissenschaft

Collaborations Workshop - CW15, March 25-27, 2015, Oxford, United Kingdom
Martin Hammitzsch, Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences
How to publish and use scientific software in the near future
› Software journals & individual policies
› Zenodo & Figshare
› Institutional repositories
quality
State of the art Near future
Challenges Approach
documentation
reproducibility
archiving
measuring
productivity
reputation
reusability executables
metrics
recognition
versioning
expertise
subject-specific
interdisciplinarity
software-specific
established
publishing
processes
proven software
engineering
practices
skills
infrastructures
and platforms
policies
merge,
test, and
evaluate
ecosystem
software publications
papers
data publications
still challenges
self-contained
X
For further reference please refer to http://dx.doi.org/10.5281/zenodo.14978

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This presentation is a part of the MosesCore project that encourages the development and usage of open source machine translation tools, notably the Moses statistical MT toolkit.   MosesCore is supported by the European Commission Grant Number 288487 under the 7th Framework Programme.     For the latest updates go to http://www.statmt.org/mosescore/ or follow us on Twitter - #MosesCore

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Presentation given at SPEC 2014, Krakow, Poland. 17-22 August 2014 [some slides do not display correctly, download the pdf for better quality] In our day-to-day practice we collect data, convert this to information, hopefully extract knowledge, and then pass this on to our peers, thereby advancing the global understanding of our field. This is a very linear process. What if we were to share our data? Have others take our information and combine it with their own? Such a branched process would likely result in more rapid discoveries and, potentially, a greater understanding. In order to facilitate data sharing we must define at least two interfaces with our peers; 1. A mechanism of them understanding the language of our data 2. A mechanism of passing on the context of our experiment Of course, both of these must work in reverse; we must understand their data and also their experimental context. These are separate yet related ideas. Our data are meaningless without context, but because we are ‘close to the action’ we do not explicitly document them. Recording the nature of our experiments can have benefits closer to home. Too often we find ourselves searching for results that we know we recorded, but have difficulty locating. Then there is the issue of recalling the exact experimental procedure involved in the sample preparation or data reduction. Documentation of these will lead to better laboratory practice all round. Earlier this year, a network of academic, clinical and industrial groups was constituted in the UK, with some international partners, to consider how best to push forward the use of infrared and Raman spectroscopies in the clinical arena: CLIRSPEC [1]. One of the work packages of the CLIRSPEC network is the development of standard protocols for data sharing. The work package falls, initially, into two parts; 1. How to easily and uniformly transfer our data between research teams and, by association, into an accessible archive. 2. How to record the provenance of our samples, the treatments they undergo, the experiments performed on them and the manner the resulting data was manipulated: the metadata. In this presentation we will outline the current position of the CLIRSPEC work package, both in terms of the performance of various candidate data formats (JCAMP-DX, SPC, netCDF, …), and the options for the recording of the metadata associated with the experimental procedure (controlled vocabularies, XML, RDF, ISA-TAB, …). Included here is the concept of a minimum reporting requirement for IR and Raman, particularly in the clinical arena, that we can all try to meet. None of this can happen without the buy-in of the community. We seek to engage everyone in a dialogue that will result in more consistent, and hopefully better, practice across all laboratories to further our understanding of clinical vibrational spectroscopy. [1] http://clirspec.org

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sciforge lightning talk at Collaborations Workshop 2015 (CW15)

1. Collaborations Workshop - CW15, March 25-27, 2015, Oxford, United Kingdom Martin Hammitzsch, Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences How to publish and use scientific software in the near future › Software journals & individual policies › Zenodo & Figshare › Institutional repositories quality State of the art Near future Challenges Approach documentation reproducibility archiving measuring productivity reputation reusability executables metrics recognition versioning expertise subject-specific interdisciplinarity software-specific established publishing processes proven software engineering practices skills infrastructures and platforms policies merge, test, and evaluate ecosystem software publications papers data publications still challenges self-contained X For further reference please refer to http://dx.doi.org/10.5281/zenodo.14978

sciforge lightning talk at Collaborations Workshop 2015 (CW15)

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