Galaxy and transmart in data management in translational research

Transcription

1 Galaxy and transmart in management in translational research Remond Fijneman, Mariska Bierkens, Sanne Abeln, Jan-Willem Boiten

2 Galaxy and transmart in management in translational research Remond Fijneman, Mariska Bierkens, Sanne Abeln, Jan-Willem Boiten

3 Topic: translational research workspace From bench to bedside

4 Translational research integration

5 Translational Research Pipeline marker identification What? marker validation assay development prospective validation cost effectiveness clinical trial test approval & implementation

6 Translational Research Pipeline n= marker identification Basic research: genomics, proteomics, metabolomics, What? marker validation Biobanks, laboratory quality systems assay development PPPs prospective validation IRBs, clinical research bureaus, consortia & networks cost effectiveness Health technology assessments clinical trial n Implementation in society; professionals patients, insurers, government test approval & implementation

7 Translational Research Pipeline marker identification Who? prospective validation assay development marker validation University Medical Centers (NFU) Research institutes (NKI-AvL, ) Public health (RIVM, TNO, SURF,..) Private partners (Pharma, Philips,..) cost effectiveness clinical trial test approval & implementation

8 Translational Research Pipeline marker identification Needed! marker validation assay development Multi-Center joint academic and private translational research efforts require sustainable IT platform for querying, viewing, and analyzing prospective validation cost effectiveness clinical trial test approval & implementation

9 Translational research IT. CTMM TraIT aims to enable translational research Process-oriented approach Avoid reinventing wheels User driven priority setting Professional support & training

10 The process Participant/ patient enters Clinical/Biobank Procedures Questionnaire EHR Imaging Samples Experiments Phenotype base Image base & analysis Biobank catalogue Experimental Data Integration External Downstream analysis Scientific Output Intellectual Property Improved Healthcare Participant Interaction

11 The process Participant/ patient enters Clinical/Biobank Procedures Questionnaire EHR Imaging Samples Experiments Phenotype base Data Capture Image base & analysis Biobank catalogue Experimental External Data Integration Data Integration Downstream analysis Scientific Output Intellectual Property Improved Healthcare Participant Interaction

12 The tools Participant/ patient enters Clinical/Biobank Procedures Questionnaire EHR Imaging Samples Experiments Phenotype base Image base & analysis Biobank catalogue Experimental Data Integration External Downstream analysis Scientific Output Intellectual Property Improved Healthcare Participant Interaction

13 The essentials Participant/ patient enters Clinical/Biobank Procedures Questionnaire EHR Phenotype base Imaging Samples Experiments FAIR (Findable, Accessible, Interoperable, Reusable) Image base & analysis Data Integration Biobank catalogue Experimental SMURF pipelines Leon Mei (Scalable, Maintainable, User friendly, Robust, Flexible) External Downstream analysis Scientific Output Intellectual Property Improved Healthcare Participant Interaction

14 FAIR is more important than tools but tools help to enforce FAIR policies

15 transmart research workspace Translational Research Data Integration& Analytics Platform

16 transmart research workspace What does the transmart research workspace support? Data warehouse for final (processed) Integration of clinical, imaging, biobanking and experimental Query and view (meta) Analyse (to some extent), export (subsets) for specific analyses Allows to trace back original (raw) and processing steps Can connect to other tools such as R and Galaxy Open source software It is free! Active international community: transmart foundation annual meetings Unmet needs? Use your resources to fill transmart functionality gaps

17 transmart research workspace How flexible should the transmart research workspace be? Data loading can not easily be fully automated supplier consult consultant curation information supplier technical loader integration consultant upload loader check information supplier technical loader integration consultant save curated state loader deployment supplier

18 transmart research workspace What works and what doesn t work for researchers? What is still missing? - Improve loading of study - Improve intuitive querying - Improve visualization & analysis

19 transmart research workspace What are the different possibilities concerning cloud and web portal solutions and what are the pros and cons? transmart is a Web Portal that provides access to your Whether your is in the cloud or at your own center does not matter..as long as security is secured (even pseudonymized patient information) Is federation of the workspace an option? Not a desirable option Data access control can be arranged Data access from different centers during analysis might be complicated

20 The tools Participant/ patient enters Clinical/Biobank Procedures Questionnaire EHR Imaging Samples Experiments Phenotype base Image base & analysis Biobank catalogue Experimental Data Integration External Downstream analysis Scientific Output Intellectual Property Improved Healthcare Participant Interaction

21 Galaxy research workspace Publish & share bioinformatics workflows Build Workflows Run Analyses Share your work Visualize your Galaxy App store: Tool Shed Demo: galaxy.ctmm-trait.nl

22 Galaxy research workspace What does the Galaxy research workspace support? Bioinformatics workflow management system, < Accessible: Users without programming experience can easily specify parameters and run tools and workflows. Reproducible: Galaxy captures information so that any user can repeat and understand a complete computational analysis. Transparent: Users share and publish analyses via the web and create Pages, interactive, web-based documents that describe a complete analysis. Open source software It is free! Active international community: Galaxy community annual meetings Unmet needs? Use your resources to fill Galaxy functionality gaps

23 Galaxy research workspace How flexible should the Galaxy research workspace be? Needs to be scalable (e.g. peak capacity during training) Needs to be secured (patient information) New tools are being developed all the time. When tools will be used on a frequent basis by non-bioinformaticians, it is worth while making them available in Galaxy What works and what doesn t work for researchers? What is still missing? Offer support to bioinformaticians to make their established workflows available Offer training to (non)-bioinformaticians to make use of existing workflows

24 Galaxy research workspace What are the different possibilities concerning cloud and web portal solutions and what are the pros and cons? Galaxy is a web-based platform that provides access to your workflows Whether your (compute) is in the cloud or at your own center does not matter..as long as security is secured (patient information) Is federation of the workspace an option? Guess so..as long as security is secured (patient information) Computational pipelines can be transferred from one site to another

25 transmart - Galaxy

26 Galaxy research workspace What does the Galaxy research workspace environment support?