Data sharing and reproducible research

A presentation given at Janelia farm during the workshop on BioImage Informatics.

1. data  sharing  and  reproducible  research barriers  and  solu-ons Satrajit Ghosh satra@mit.edu Massachusetts Institute of Technology
2. problems solutions future barriers to data and code sharing current approaches in neuroimaging can we have reproducible research?
3. problems solution future let’s step backwards Oliver Doehermann, Anisha Keshavan, Franzi H.
4. problems solution future let’s step backwards Train Test SPM Extract Cluster Means Linear Regression Predict Step 1: Split data into a training and test set Step 2: Find significant clusters Step 3: Extract mean intensity for the test and training sets Step 4: Use training data to run a linear regression Step 5: Use the model and the test data to predict lsas‐Δ score. Folds Data Oliver Doehermann, Anisha Keshavan, Franzi H.
5. problems solution future let’s step backwards Train Test SPM Extract Cluster Means Linear Regression Predict Step 1: Split data into a training and test set Step 2: Find significant clusters Step 3: Extract mean intensity for the test and training sets Step 4: Use training data to run a linear regression Step 5: Use the model and the test data to predict lsas‐Δ score. Folds Data Oliver Doehermann, Anisha Keshavan, Franzi H.
6. problems solution future let’s step backwards Train Test SPM Extract Cluster Means Linear Regression Predict Step 1: Split data into a training and test set Step 2: Find significant clusters Step 3: Extract mean intensity for the test and training sets Step 4: Use training data to run a linear regression Step 5: Use the model and the test data to predict lsas‐Δ score. Folds Data Oliver Doehermann, Anisha Keshavan, Franzi H.
7. problems solution future let’s step backwards Train Test SPM Extract Cluster Means Linear Regression Predict Step 1: Split data into a training and test set Step 2: Find significant clusters Step 3: Extract mean intensity for the test and training sets Step 4: Use training data to run a linear regression Step 5: Use the model and the test data to predict lsas‐Δ score. Folds Data Oliver Doehermann, Anisha Keshavan, Franzi H.
8. problems solution future let’s step backwards Train Test SPM Extract Cluster Means Linear Regression Predict Step 1: Split data into a training and test set Step 2: Find significant clusters Step 3: Extract mean intensity for the test and training sets Step 4: Use training data to run a linear regression Step 5: Use the model and the test data to predict lsas‐Δ score. Folds Data Oliver Doehermann, Anisha Keshavan, Franzi H.
9. problems solution future let’s step backwards Train Test SPM Extract Cluster Means Linear Regression Predict Step 1: Split data into a training and test set Step 2: Find significant clusters Step 3: Extract mean intensity for the test and training sets Step 4: Use training data to run a linear regression Step 5: Use the model and the test data to predict lsas‐Δ score. Folds Data Oliver Doehermann, Anisha Keshavan, Franzi H.
10. problems solution future let’s step backwards Train Test SPM Extract Cluster Means Linear Regression Predict Step 1: Split data into a training and test set Step 2: Find significant clusters Step 3: Extract mean intensity for the test and training sets Step 4: Use training data to run a linear regression Step 5: Use the model and the test data to predict lsas‐Δ score. Folds Data Enough details? Oliver Doehermann, Anisha Keshavan, Franzi H.
11. problems solution future let’s step backwards Train Test SPM Extract Cluster Means Linear Regression Predict Step 1: Split data into a training and test set Step 2: Find significant clusters Step 3: Extract mean intensity for the test and training sets Step 4: Use training data to run a linear regression Step 5: Use the model and the test data to predict lsas‐Δ score. Folds Data Enough details? No Oliver Doehermann, Anisha Keshavan, Franzi H.
12. problems solution future let’s step backwards
13. problems solution future let’s step backwards What else? Where did the input data come from? What procedure was used to collect clinical data? What were the process parameters?
14. problems solution future the scientific process Generate hypotheses Design experiment Collect data Analyze data Interpret results Publish
15. problems solution future the scientific process Generate hypotheses Design experiment Collect data Analyze data Interpret results Publish 18% 9% 18% 27% 9% 18% Hypothesize Design Collect Analyze Interpret Publish dramatization. not to be taken too seriously
16. Slice  6ming   correc6on Realignment   (to  first  image) Func6onal   data Structural     data Skull  stripping (FSL) Bias  correc6on (SPM2) Normaliza6on (SPM2   template) Smoothing   (4mm  FWHM) Normaliza6on Coregistra6on problems solution future replicating methods
17. Slice  6ming   correc6on Realignment   (to  first  image) Func6onal   data Structural     data Skull  stripping (FSL) Bias  correc6on (SPM2) Normaliza6on (SPM2   template) Smoothing   (4mm  FWHM) Normaliza6on Coregistra6on problems solution future replicating methods
18. problems solution future the metamorphosis
19. Structural Diffusion Functional problems solution future the metamorphosis
20. Structural Diffusion Functional problems solution future the metamorphosis
21. ? Structural Diffusion Functional problems solution future the metamorphosis
22. ? Structural Diffusion Functional problems solution future the metamorphosis
23. problems solution future the world of neuroimaging analysis software data source: pymvpa.org 1990 92 94 96 98 2000 02 04 06 08 2010 Afni Brainvoyager Freesurfer R Caret Fmristat FSL MVPA NiPy ANTS SPM Brainvisa
24. different algorithms different assumptions different platforms different interfaces different file formats problems solution future the world of neuroimaging analysis software data source: pymvpa.org 1990 92 94 96 98 2000 02 04 06 08 2010 Afni Brainvoyager Freesurfer R Caret Fmristat FSL MVPA NiPy ANTS SPM Brainvisa
25. problems solution future the scientific process “The scientific method’s central motivation is the ubiquity of error - the awareness that mistakes and self-delusion can creep in absolutely anywhere and that the scientist’s effort is primarily expended in recognizing and rooting out error.” Donoho et al. (2009) assumed veracity of publications dependence on peer review as a proxy for testing
26. problems solution future but why share data and code?
27. special populations : problems solution future but why share data and code?
28. special populations : enables aggregation of large data sets problems solution future but why share data and code?
29. special populations : enables aggregation of large data sets (e.g., Autism, ADHD, Schizophrenia) problems solution future but why share data and code?
30. special populations : enables aggregation of large data sets (e.g., Autism, ADHD, Schizophrenia) cross-discipline interaction : problems solution future but why share data and code?
31. special populations : enables aggregation of large data sets (e.g., Autism, ADHD, Schizophrenia) cross-discipline interaction : - provides data to test their algorithms problems solution future but why share data and code?
32. special populations : enables aggregation of large data sets (e.g., Autism, ADHD, Schizophrenia) cross-discipline interaction : - provides data to test their algorithms - increases sample size for learning algorithms problems solution future but why share data and code?
33. special populations : enables aggregation of large data sets (e.g., Autism, ADHD, Schizophrenia) cross-discipline interaction : - provides data to test their algorithms - increases sample size for learning algorithms pedagogy : problems solution future but why share data and code?
34. special populations : enables aggregation of large data sets (e.g., Autism, ADHD, Schizophrenia) cross-discipline interaction : - provides data to test their algorithms - increases sample size for learning algorithms pedagogy : provides easy mechanism to train new personnel problems solution future but why share data and code?
35. problems solution future current barriers
36. most publications do not include data, code problems solution future current barriers
37. most publications do not include data, code some journals mandate but provide no infrastructure for storage, distribution problems solution future current barriers
38. most publications do not include data, code some journals mandate but provide no infrastructure for storage, distribution most scientists do not have the time to curate data problems solution future current barriers
39. most publications do not include data, code some journals mandate but provide no infrastructure for storage, distribution most scientists do not have the time to curate data no standard ontology for describing experiments, data, derived data, workflows problems solution future current barriers
40. problems solution future other practical matters
41. how to share data/code? problems solution future other practical matters
42. how to share data/code? what to share? problems solution future other practical matters
43. how to share data/code? what to share? where to share? problems solution future other practical matters
44. how to share data/code? what to share? where to share? how to include manual intervention? problems solution future other practical matters
45. problems solutions future barriers to data and code sharing current approaches in neuroimaging can we have reproducible research?
46. problems solution future data sharing Neuroimaging Tools and Resources Clearinghouse (NITRC) XNAT (Wash U) + HID (BIRN) + IDA (LONI) databases Brain Map (brainmap.org) National Database for Autism Research (NDAR) Personal web sites
47. ipython scipy + numpy networkx sympy matplotlib mayavi + tvtk problems solution future open-source scientific computing stack
48. problems solution future code sharing: formalized interfaces and workflows Neuroimaging Pipelines and Interfaces nipy.org/nipype
49. problems solution future part of a family
50. problems solution future nipype: components
51. problems solution future nipype: components
52. problems solution future nipype: workflow engine
53. problems solution future nipype: execution plugins
54. problems solution future nipype
55. problems solution future using nipype: integrating across packages
56. problems solution future capturing provenance: open provenance model
57. problems solution future capturing provenance: open provenance model
58. problems solution future capturing provenance: open provenance model
59. problems solutions future barriers to data and code sharing current approaches in neuroimaging can we have reproducible research?
60. problems solution future technical options Electronic computable notebooks (cdf : computable document format) Virtual environments Standard ontology Formalized interfaces Federated databases