The SEEK: a platform for sharing data and models in systems biology

Published on 2012-11-234785 Views

Systems biology research is typically performed by multidisciplinary groups of scientists, often in large consortia and in distributed locations. The data generated in these projects tend to be hetero

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Presentation

The SEEK: a platform for sharing data and models in systems biology00:00

SysMO-SEEK: Platform and Service07:40:52

SysMO-SEEK History17:08:40

Types of data38:58:55

No one concept of experimentation or modelling49:11:52

SysMO-DB54:23:01

SysMO-DB Team74:20:36

Social and technical challenges95:30:49

Systems Biology = Integration135:30:34

Integration needs communication147:08:42

Communication important159:43:51

Analysis of SySMO Requirements179:04:29

Results193:59:44

Social Approach220:10:31

SysMO-SEEK: an integration platform259:04:23

JERM – Just Enough Results Model293:16:17

JERM309:56:29

"MIBBI" for SysMO327:51:09

Data - what have we found? - 1351:39:51

Data - what have we found? - 2378:25:13

Data - what have we found? - 3379:16:16

Data - what have we found? - 4390:29:21

Data - what have we found? - 5406:02:41

Data - what have we found? - 6414:14:54

Motivation to use Standards419:08:51

http://www.mibbi.org/index.php/MIBBI_portal439:21:06

Following Standards454:22:28

Experimental Processes503:02:05

MASTER template(s)504:26:54

Data sheet / Results sheet529:19:13

Instruments sheet544:32:31

Biosamples sheet552:55:20

VLN specific metadata templates568:56:49

ISA - a common framework for describing how different types of data relates to its experimental context608:13:42

A Packaged Tree View628:07:04

RightField template generation655:16:56

RightField: Semantic Annotation by Stealth660:24:41

RightField684:13:18

Metadata Extraction and Querying697:40:10

JERM templates: where to find them? - 1706:45:57

JERM templates: where to find them? - 2713:12:25

JERM templates: where to find them? - 3717:31:08

Screenshot - 1720:13:23

Screenshot - 2725:27:46

Screenshot - 3731:17:42

ISA example from SySMO/ MOSES735:43:17

Screenshot - 4746:53:49

Just Enough Sharing756:19:08

Visibility rules?768:10:15

Explore and annotate data769:05:24

VLN Extensions775:29:03

Access other resources through a SEEK - 1783:30:52

Model curation: SEEK and JWS Online784:31:35

JWS OneStop to Model Standards787:07:57

Access other resources through a SEEK - 2791:31:26

Access other resources through a SEEK: BioModels793:09:00

Integration of SYCAMORE into SEEK796:57:22

Integration of Cytoscape798:18:56

Access other resources through a SEEK - 3800:00:19

Database Population and Access808:34:25

SBML export from SABIO-RK809:22:52

Integration of SabioRK into SEEK - 1809:53:26

Integration of SabioRK into SEEK - 2818:36:25

Examples of Taverna Workflows for Systems Biology825:32:37

What do Scientists use Taverna for?829:52:25

High Throughput Experiments830:25:56

Mapping transcriptomics data onto SBML models842:27:59

Reuse, Recycle, Repurpose Workflows843:00:31

Training and Know-how843:20:52

Teaching, training864:46:32

http://www.seek4science.org/869:23:11

Current and Future Work871:39:22

SEEK adoption877:40:28

The Team897:11:49

Acknowledgements909:25:34