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The SEEK: a platform for sharing data and models in systems biology
Published on Nov 23, 20124788 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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Chapter list
The SEEK: a platform for sharing data and models in systems biology00:00
SysMO-SEEK: Platform and Service00:27
SysMO-SEEK History01:01
Types of data02:20
No one concept of experimentation or modelling02:57
SysMO-DB03:15
SysMO-DB Team04:27
Social and technical challenges05:43
Systems Biology = Integration08:07
Integration needs communication08:49
Communication important09:35
Analysis of SySMO Requirements10:44
Results11:38
Social Approach13:12
SysMO-SEEK: an integration platform15:32
JERM – Just Enough Results Model17:35
JERM18:35
"MIBBI" for SysMO19:40
Data - what have we found? - 121:05
Data - what have we found? - 222:42
Data - what have we found? - 322:45
Data - what have we found? - 423:25
Data - what have we found? - 524:21
Data - what have we found? - 624:51
Motivation to use Standards25:08
http://www.mibbi.org/index.php/MIBBI_portal26:21
Following Standards27:15
Experimental Processes30:10
MASTER template(s)30:16
Data sheet / Results sheet31:45
Instruments sheet32:40
Biosamples sheet33:10
VLN specific metadata templates34:08
ISA - a common framework for describing how different types of data relates to its experimental context36:29
A Packaged Tree View37:41
RightField template generation39:19
RightField: Semantic Annotation by Stealth39:37
RightField41:03
Metadata Extraction and Querying41:51
JERM templates: where to find them? - 142:24
JERM templates: where to find them? - 242:47
JERM templates: where to find them? - 343:03
Screenshot - 143:12
Screenshot - 243:31
Screenshot - 343:52
ISA example from SySMO/ MOSES44:08
Screenshot - 444:48
Just Enough Sharing45:22
Visibility rules?46:05
Explore and annotate data46:08
VLN Extensions46:31
Access other resources through a SEEK - 147:00
Model curation: SEEK and JWS Online47:04
JWS OneStop to Model Standards47:13
Access other resources through a SEEK - 247:29
Access other resources through a SEEK: BioModels47:35
Integration of SYCAMORE into SEEK47:49
Integration of Cytoscape47:53
Access other resources through a SEEK - 348:00
Database Population and Access48:30
SBML export from SABIO-RK48:33
Integration of SabioRK into SEEK - 148:35
Integration of SabioRK into SEEK - 249:06
Examples of Taverna Workflows for Systems Biology49:31
What do Scientists use Taverna for?49:47
High Throughput Experiments49:49
Mapping transcriptomics data onto SBML models50:32
Reuse, Recycle, Repurpose Workflows50:34
Training and Know-how50:36
Teaching, training51:53
http://www.seek4science.org/52:09
Current and Future Work52:17
SEEK adoption52:39
The Team53:49
Acknowledgements54:33