Mobile lab app

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Talk given at Garscube on the 12th Dec 2012 explaining Nachiket Khandetod computer science project and a future project on linking data together.

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  • The idea of a digital lab is decades old but now that tablets have become cheap, it seems that the moment has come where everybody can start benefiting from them.I think that these devices are likely to change the way we work in the same way as PCs have helped our productivity.But although the hardware is important, the most important is that we are able to get a better grasp of our data.
  • Ability to provide remote access to digital record keeping could lead to exciting developments
  • Valuable lessons learnt, although googledocs has the advantage that the database is being managed by Google it has limitations.
  • Linked DataThe Semantic Web isn't just about putting data on the web. It is about making links, so that a person or machine can explore the web of data.  With linked data, when you have some of it, you can find other, related, data.Like the web of hypertext, the web of data is constructed with documents on the web. However,  unlike the web of hypertext,  where links are relationships anchors in hypertext documents written in HTML, for data they links  between arbitrary things described by RDF,.  The URIs identify any kind of object or  concept.   But for HTML or RDF, the same expectations apply to make the web grow:Use URIs as names for things Use HTTP URIs so that people can look up those names. When someone looks up a URI, provide useful information, using the standards (RDF*, SPARQL) Include links to other URIs. so that they can discover more things. What is linked data:Linked Data refers to data published on the Web in such a way that it is machine-readable, its meaning is explicitly defined, it is linked to other external data sets, and can in turn be linked to from external data sets Advantages:helping developers integrate data into their applications. And, by following links in the dataset, we can discover more useful data
  • We have systems within the lab and the CVR as whole that, historically, have not easily interoperated at the data level
  • So
  • For example, Pablo is currently leading a project on the possible spillover of avian influenza into the horse population in Mongolia and China. Keeping up to date on the various experiments taking place and the different viruses that different researchers are using is difficult.
  • Semantic MediaWiki is also a full-fledged framework, in conjunction with many spinoff extensions, that can turn a wiki into a powerful and flexible “collaborative database”. All data created within SMW can easily be published via the Semantic Web, allowing other systems to use this data seamlessly.
  • http://www.bbsrc.ac.uk/news/people-skills-training/2011/110510-f-innovators-pt1-swedlow.aspx
  • Could the new building be the embodiment of the lab of the future?
  • Mobile lab app

    1. 1. The digital labTowards improving workflows and linking data
    2. 2. The Times They Are a-Changin’ Bob Dylan• 46% of Americans and 25% of adults in the UK own a smartphone• 85% of medical professionals use smartphones• 30-50% use apps in their clinical practice Buijink et al. (2012)Evid Based Med.
    3. 3. Nature Vol 481 | 26 Jan 2012
    4. 4. Outline• Proto-type mobile app Nachiket Khandetod• Future project: Linking data François Gonzalez
    5. 5. LousebaseMultiple excel Microsoft MySQL and Googlespreadsheets access ColdFusion spreadsheets
    6. 6. Google spreadsheets http://goo.gl/6ilXf
    7. 7. SpecimenCode SpecimenCode ExtractionCodeGenus Extraction Code PrimerNameSpecies Name Date Extracted GeneBoxNo AmplificationBoxColumn SentToSequencingHost GenusHost Species PrimerNameLatitude PrimerSequenceLongitude GeneCollectedBySex ExtractionCode Gene Accession Sequence
    8. 8. Proto-type app
    9. 9. Limitations of using GoogleDocs• Restricted to their own API• Slow• Limitations to multiple users unless $$$
    10. 10. Linked data = the semantic web Tim Berners-Lee 2006
    11. 11. HI assay Trachea experiments Images Bead assays Virus quantification Sequences>Hu_NA_AAF77036_H1N1MNPNQKIITIGSICMVVGIISLILQIGNIISIWVSHSIQTGNQNHPETCNQSIITYENNTWVNQTYVNISNTNVVAGQDATSVILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVI Currently, we have rather unlinkedREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESEC data within the labACVNGSCFTIMTDGPSNGQASYKILKIEKGKVTKSIELNAPNYHYEECSCYPDTGKVMCVCRDNWHGSNRPWVSFDQNLDYQIGYICSGVFGDNPRPNDGTGSCGPVSSNGANGIKGFSFRYDNGVWIGRTKSTSSRSGFEMIWDPNGWTETDSSFSVRQDIVAITDWSGYSGSFVQHPELTGLDCMRPCFWVELIRGQPKENT-IWTSGSSISFCGVNSDTVGWSWPDGAELPFSIDK
    12. 12. Answering simple questions becomes time consuming• Give me all the work that has been done in the lab on virus X?• How does virus X grow in trachea and react for horse serum in HI assays?• Which viruses have been studied in trachea but not sequenced?
    13. 13. mallard_CzechRepublic_13577-24K_16-09-2010 N-type Titers HI TracheaExpt MN11F_2076_H3_consensus_sequence N8 256 Yes Yes 80 29 duck_Italy_194659_01-01-2006 66 Anasplatyrhynchos_Belgium_12827_18-09-2007 37 pelican_Zambia_01_01-08-2006 73 17 duck_Zambia_04_01-06-2008 99 goose_Zambia_05_01-07-2008 Stellerseider_Alaska_44222-192_06-09-2006 canine_Guangdong_2_18-10-2007 100 canine_Jiangsu_01_01-12-2009 58 48 canine_Korea_01_2007 chicken_Vietnam_G14_01-01-2008 100 duck_Guangdong_W12_2011 MN09_881V_H3_consensus_sequence N8 x x Yes 100 MN09_882V_H3_consensus_sequence N8 512 x x duck_Vietnam_G119_01-11-200661 65 MN11F_1787_H3_consensus_sequence N8 x Yes x 42 duck_Beijing_61_01-01-2005 3 38 MN10F_1551_H3_consensus_sequence N1 512 x x 17 MN09_969V_H3_consensus_sequence N8 x x x 29 54 43 8 MN10F_1906_H3_consensus_sequence N8 x x x MN11F_2157_H3_consensus_sequence N3 128 x x 96 87 MN10F_1581_H3_consensus_sequence N8 128 x x redcrestedpochard_Mongolia_1915_19-09-2006 53 MN11F_2185_H3_consensus_sequence N8 256 x Yes 99 100 MN11F_1782_HA_consensus_sequence N8 (N2) x x x 100 MN11F_2106_H3_consensus_sequence N8 128 Yes Yes MN11F_2377_H3_consensus_sequence N6 x x x 63 MN09_963V_H3_consensus_sequence N8 512 Yes Yes 45 MN09_973V_H3_consensus_sequence 100 N8 256 x x 86 MN09_961V_H3_consensus_sequence N8 128 x x 70 9 7 MN09_977V_H3_consensus_sequence N8 256 x Yes MN09_957V_H3_consensus_sequence ? 256 x x MN11F_2271_H3_consensus_sequence N8 256 Yes Yes 100 MN09_899V_H3_consensus_sequence N6 x x x equine_Jilin_1_1989 100 Equine_HeilongJiang_12_1990 0.02
    14. 14. Trachea Expt HI AsaysDog VirusTrachea Blood TypeVirus SerumQuantification Positive/Negative Staining Expt SequencingTracheaStaining VirusImage Sequence methodPositive/Negative Assembly method Sequence Apoptosis Histological changes
    15. 15. OMEOpen Microscopy Environment
    16. 16. Future opportunities• New building, new approach to record keeping• More data stored, more data shared between labs

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