2/15/2016. PAL`s experience - IMOMESIC Project
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1 2/15/2016 PAL`s experience - IMOMESIC Project
2 Page2 Content Why Data management and PAL activities? Who is doing it? What are we doing? Encountered problems and issues Outlook
3 Page3 Why Data management and PAL activities? PAL (Project Liason Officer = Contact person / mediator for experimentalists, modelers and software developer) Protection from data loss 3 HDDs defect in 12 month Data is stored on private data storage Findable, Accessible, Interoperable and Reusable (FAIR) Data Data is stored locally or unstructured Data is not annotated Annotations are not standardized Data is not available to partners / no communication Financial and time benefits Experiments are done twice Searching for data takes time (hours - days) Wrong interpretation of data Copy and paste errors
4 Page4 Why Data management and PAL activities? PAL (Project Liason Officer = Contact person / mediator for experimentalists, modelers and software developer) Protection from data loss 3 HDDs defect in 12 month Data is stored on private data storage Findable, Accessible, Interoperable and Reusable (FAIR) Data Data is stored locally or unstructured Data is not annotated Annotations are not standardized Data is not available to partners / no communication Financial and time benefits Experiments are done twice Searching for data takes time (hours - days) Wrong interpretation of data Copy and paste errors
5 Page5 Why Data management and PAL activities? PAL (Project Liason Officer = Contact person / mediator for experimentalists, modelers and software developer) Protection from data loss 3 HDDs defect in 12 month Data is stored on private data storage Findable, Accessible, Interoperable and Reusable (FAIR) Data Data is stored locally or unstructured Data is not annotated Annotations are not standardized Data is not available to partners / no communication Financial and time benefits Experiments are done twice Searching for data takes time (hours - days) Wrong interpretation of data Copy and paste errors
6 Page6 Why Data management and PAL activities? PAL (Project Liason Officer = Contact person / mediator for experimentalists, modelers and software developer) Protection from data loss 3 HDDs defect in 12 month Data is stored on private data storage Findable, Accessible, Interoperable and Reusable (FAIR) Data Data is stored locally or unstructured Data is not annotated Annotations are not standardized Data is not available to partners / no communication Financial and time benefits Experiments are done twice Searching for data takes time (hours - days) Wrong interpretation of data Copy and paste errors
7 Page7 Why Data management and PAL activities? PAL (Project Liason Officer = Contact person / mediator for experimentalists, modelers and software developer) Protection from data loss Findable, Accessible, Interoperable and Reusable (FAIR) Data 3 HDDs defect in 12 month Data is stored on private data storage It is good to have one or more PALs who are responsable for data management Saves you money, time and stress Data is stored locally or unstructured Data is not annotated Annotations are not standardized Data is not available to partners / no communication Financial and time benefits Experiments are done twice Searching for data takes time (hours - days) Wrong interpretation of data Copy and paste errors
8 Page8 Who is doing it? Integrating Modeling of Metabolism and Signalling towards an Application in Liver Cancer Application in medicine 7 partners from metabolomics, proteomics and genomics PALs Markus Stepath / Experimantalist Joep Vanlier / modelling background Avlant Nilsson / modelling background FAIRDOM team and supporters All areas (modellers and experimentalists) are covered Support from FAIRDOM team is straightforward and steadily Olga Krebs Rostyslav Kuzyakiv scientific IT service of the ETH Zürich IT core facility DKFZ Hits Wolfgang Müller Andreas Weidemann...
9 Page9 What are we doing? Optimizing data storage Implementing standardized and controlled vocabulary/formats to integrate data (JERM, MIBBI, SBML, ) Ensure that data is findable, accessible, interoperable and reusable (long term perspective) Teaching users Communicate with users SEEK OpenBIS Excemplify Antibody Database Sharing of results, presentations, SOPs & Organization of events Storage and analysis of Mass spectrometry data (proteomics) Storage and handling of IMMUNOBLOT, qpcr and LUMINEX data Database for all antibodies in our lab (>700 entries) SEEK server, access via browser Local server, access via browser Local server, access via browser Local server, access via browser
10 Page10 SEEK
11 Page11 OpenBIS
12 Page12 Excemplify Excemplify (= Excel + Simplify) in Klingmüller s Lab User-friendly database Web based application Main functions of Excemplify: Storage and sharing of experimental data and meta information in a standardized way Support of experimentalists in the data handling procedure and data submission Minimized copy and paste errors Reduced time to find data across experimentalists / projects (search function & standardized metadata/annotations) Connected to SEEK Wizard for experimental design
13 Page13 Antibody Database Storage location, amount, product information, users, Costs for Data management & Databases [ / year ] openbis Antibody Database Data storage 4398
14 Page14 Antibody Database Storage location, amount, product information, users, Costs for Data management & Databases [ / year ] No more double orderings or hidden supplies Spendings saved per year for antibodies: ~10% (~10,000 )) Minimized time to find antibodies openbis Antibody Database Data storage 4398
15 Page15 Encountered problems and issues User commitment this needs to much time! it s too complicated! I did it always like that! Willingness to share data is limited and it is difficult to convince researchers to share raw data even after publication Disprove make belief Communication with users Make software tools as simple as possible (e.g.: wizard) DOIs for raw data
16 Page16 Outlook Implementation of openbis in our daily workflow
17 Thank you for your attention! Further information on
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