andrew treloar - the life‐sciences as a pathfinder in data‐intensive research practice abstract:...
DESCRIPTION
The advent of the Internet is bringing about fundamental changes in the ways that research is performed and communicated. These have been particularly driven by the growing importance of data, as well as the tools available to work with this data. This presentation will examine this shift, drawing on examples from the life‐sciences, and try to make some predictions about the next five years. First presented at the 2014 Winter School in Mathematical and Computational Biology http://bioinformatics.org.au/ws14/program/TRANSCRIPT
The life-‐sciences as a pathfinder in data-‐intensive research prac3ce Dr Andrew Treloar, Director of Technology
July 10, 2014 CC-‐BY-‐SA, @atreloar 1
Structure presenta3on § Research Lifecycles § Func3ons of Scholarly Communica3on § Pointers to the future § Characterising the future § Pathfinder problems § Conclusions
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So many lifecycles…
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Minimal Research Lifecycle
Think
Do Share
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Sharing: Scholarly Communication System and its Functions § Registration § Certification § Awareness § Archiving
(Rosendaal and Geurts, 1997)
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System of Journals § Registration
§ submission of manuscript § Certification
§ peer-review (pre-publication) § commentary (post-publication)
§ Awareness § discovery services
§ Archiving § libraries (print) § publishers (electronic) § special purpose organisations (e.g. Portico)
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Pointers to the future
“the future is already here – it’s just not very evenly distributed”
William Gibson, NPR interview
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Registration: BioRxiv
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Registration: Github
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Registration: WikiPathways
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Registration: NeuroLex
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Registration: Nanopublications
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Registra3on: some observa3ons § Decoupling registra3on from cer3fica3on § Timestamping, versioning § Registra3on of various types of objects § Machines as creators and contributors
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Certification: PubMed Commons
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Certification: PubPeer
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Cer3fica3on: Publons
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Cer3fica3on: some observa3ons § Peer-‐review decoupled from publica3on process § Cer3fica3on of various types of objects § Machines valida3ng form § Social endorsement
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Awareness: myExperiment
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Awareness: eLabNotebook RSS
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Awareness: Twitter
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Awareness: some observations § Awareness for various types of objects § Real 3me awareness § Awareness support targeted at machines § Awareness through social media
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Archiving: PDB
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Archiving: GenBank
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Characterising the future
Fixed Varying
Discrete Continuous
Hidden VisibleResearch Process
Nature of object
Process of making public
Speed of communicationDelayed Instant
Atomic CompoundAtomicity of object
Communicated objectPublication
+data proxies
Publication + linked data + linked models
Formal InformalNature of processJuly 10, 2014 CC-‐BY-‐SA, @hvdsomp and @atreloar 24
Fundamental changes § The research process (objects, social
dimension) is becoming more exposed § Articles, books are no longer the only
relevant objects for research communication
§ Objects are no longer static § Machines are joining humans as
(co-)creators and consumers of research objects
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Pathfinder problems § Integrity of the scholarly record § The three obsolescences
§ hardware § file format § soWware
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System of Journals: Archiving
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Web of Objects: Archiving?
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Not just citation relationships
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The problem of obsolescence § Lifescience research environment can be viewed as undergoing a process of accelerated evolu3on
§ Other disciplines will hit these problems in 3me
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Cambrian explosion
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Hardware obsolescence: Roche 454
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SoWware obsolescence: too much choice, not enough support
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Abandonware § “Last summer, a member of the biology department of the
University of Udine in Italy approached Nicola Vitacolonna with an intriguing project. The ANREP program, which annotates structural mo3fs in gene or protein sequences, was out of date having been wriben more than a decade ago. Although s3ll used by molecular biologists, its slow compu3ng ability meant a straighcorward mul3ple search could take all night on a desktop PC. The Udine biologist wanted Vitacolonna, a postdoctoral fellow in computa3onal biology, to write a program that could do the job more quickly.” § Sam Jaffe, Scien3sts Abandon their SoWware, The Scien)st, Feb 16, 2004
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File format obsolescence: Illumina § Probability of error in basecalling encoded using ascii code to reduce file size
§ Meaning of the ascii code changed along the life cycle and for data generated at different 3me points the quality might be encoded differently
§ “If you get an error like "Invalid quality score value", your fastq file probably has Sanger (offset 33) instead of Illumina (ASCII offset 64) quality scores. You'll need to add the op3on "-‐Q33" to your FASTX Toolkit arguments”. Obviously…
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Evereb Rogers, Diffusion of Innova)on, 1962
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Conclusions § Need to move to a smaller number of standard file formats
§ Need to move to a more sustainable model of soWware development and maintenance
§ Need to encourage placorm manufacturers to innovate around the hardware, not the soWware
§ NOTE: other disciplines are looking to lifesciences to work out how to solve some of these problems
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On best prac3ces in the development of bioinforma3cs soWware, Front. Genet., 02 Jul 14
§ Source code available to reviewers § SoWware indexed, citable, available § Source code documented § Source code managed § Test libraries, sample data and dataset repositories available
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Ques3ons? § [email protected]
§ @atreloar § hbps://www.slideshare.net/atreloar/the-‐lifesciences-‐as-‐a-‐pathfinder-‐in-‐dataintensive-‐research-‐prac3ce
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