1. PipeWork and Selector Raymond Ripp

2. A simple PipeWork : Calculette Add Output

3. Enter the values and press Add Output 4 5 = 9

4. Predefined inputs Add Output 5

5. Edit the PipeWork Add Output Multiply

6. Processing Elements Processing Element Output Any php function With 0, 1, 2, … n arguments One output Defined in class PW:: Security Centralisation Adaptation Reflection

7. Processing Elements 1/6 HtmlTable Html PWSessionVariables PWMultipleSelectFrom_listOfPW PWselectFrom_listOfPW PWlistOfPW PWcompareArray PWsearchInAllPipeWorks PWsearchReplaceInAllPipeWork PWdate PWappend PWmemo PWnop PWswitchBetween PWisLess PWisLessOrEqual PWisEqual PWisDifferent PWisGreaterOrEqual PWisGreater PWdecrement PWadd PWdivide PWmultiply PWsubstract PWemptyString PWcount PWarrayDiff PWemptyArray PWtoArray

8. Processing Elements 2/6 PWappendToArray PWcombine PWfromArray PWsubArrayTabulated PWsubArray PWsubArray0 PWsubArray1 PWsubArray2 PWsetInArray PWset2InArray PWsplitInWordsWithSemiColon PWsplitInWordsWithComma PWsplitInWords PWsplitInLines PWfirstWordOfLines PWfirstWordsInArray PWbrowse PWenter PWselect PWtext PWselectFrom_ListOfYesNo PWListOfYesNo PWselectFrom_ListOfUnionInterA notBnotA PWListOfUnionInterAnotBnotA PWarrayOfSubElement PWlowercase PWUnionInterAnotBnotA PWintersection PWunion4 PWunion PWinAnotB PWinBnotA PWsort PWreindex PWunique PWuniqueReindex PWinArray

9. Processing Elements 3/6 PWtoStore PWdeleteStore PWfromStore PWfileOfStore PWnameOfStore PWdirOfStore PWMultipleSelectFrom_listOfStoreX PWselectFrom_listOfStoreX PWlistOfStoreX PWMultipleSelectFrom_listOfStore PWselectFrom_listOfStore PWlistOfStore

10. Processing Elements 4/6 GXClusterList GXClusterComposition GXMultipleSelectFrom_listOfTissue GXselectFrom_listOfTissue GXlistOfTissue GXTissue GXselectFrom_listOfProbesetsOfGeneList GXlistOfProbesetsOfGeneList GXselectFrom_listOfProbesetsOfGeneName GXlistOfProbesetsOfGeneName GXMultipleSelectFrom_listOfRealExp GXselectFrom_listOfRealExp GXlistOfRealExp GXProbesetFromRealexp GXProbesetFromRealexpSoftware GXProbesetFromArraytype GXProbesetsConcerning GXProbeset GXManageRealExp GXRealExp GXselectFrom_listOfArraytype GXlistOfArraytype GXArraytype GXDbInput GXselectFrom_listOfGxDbInput GXlistOfGxDbInput GXselectFrom_listOfAffyAnnotFiles GXlistOfAffyAnnotFiles GXselectFrom_listOfIndividual GXlistOfIndividual GXIndividual GXselectFrom_listOfGenotype GXlistOfGenotype GXGenotype GXselectFrom_listOfOrganism GXlistOfOrganism GXOrganism etc.

11. Processing Elements 5/6 ImAnnoListOfAnnotatedGPaintGene ImAnnoGPaintGene ImAnnoGPaintGenes ImAnnoSelectFrom_ListOfGPaintGene ImAnnoListOfGPaintGene ImAnnoSelectFrom_TissueType ImAnnoTissueType ImAnnoSelectFrom_ListOfTissueType ImAnnoListOfTissueType ImAnnoSelectFrom_ListOfSieve ImAnnoListOfSieve ImAnnoSelectFrom_ListOfSieveEye ImAnnoListOfSieveEye ImAnnoListOfSieveEar ImAnnoFromSieves ImAnnoFromSieve ImAnnoCorrelateTissues ImAnnoCadre ImAnnoOrgan ImAnnoSelectFrom_ListOfCadre ImAnnoListOfCadre ImAnnoSelectFrom_ListOfOrgan ImAnnoListOfOrgan ImAnnoCreateSieve ImAnnoSelectFrom_ListOfEGEKeys ImAnnoListOfEGEKeys ImAnnoListOfEGEHeader ImAnnoEGE

12. Processing Elements 6/6 Go GoSelectFrom_ListOfAction GoListOfAction GoSelectFrom_ListOfFields GoListOfFields AmdCommon FedMultipleSelectFrom_ListOfGrog FedSelectFrom_ListOfGrog FedListOfGrog FedGrogTable FedPeople FedSelectFrom_ListOfPeopleFields FedListOfPeopleFields FedDatafile FedSelectFrom_ListOfDatafileFields FedListOfDatafileFields Wscope …

13. Enter - Select - MultipleSelect

14. Select and fill in the enter values

15. … the MultipleSelect … and Press the orange button.

16. … in graphical mode. Output type name AlsaChip manufacturer probesetcount keywords Bad Good Cheep description Bla bla url chips Chicken action update ArrayType

17. Create Edit Manage PipeWorks

18. Store and Restore Every data can be stored as a php serialized data … and restored

19. What is in the pipes ? Numbers Texts Arrays Objects All what the Working Elements can manage

20. Managing arrays PWemptyArray PWtoArray PWappendToArray PWcombine PWfromArray PWsubArray PWsplitInWords PWsplitInLines PWfirstWordOfLines PWfirstWordsInArray PWintersection PWunion PWinAnotB PWinBnotA PWsort PWreindex PWunique PWuniqueReindex PWinArray etc.

21. GX Radar Generator

22. ImAnno Gene List How to combine list of genes from ImAnno search tool through sieves (using ImAnno SQL query) Transcriptomic Expression (GscopeWebService) Diseases related genes (serialized stores) With Union, Intersection, AnotB, etc.

23. sieves Cochlea Sacculus Utriculus url Select Store cochlea sacculus utriculus other Select Disease Jax Ihr Sanger All ISH Annotation Intersection GenePaintGenes Information Intersection Transcriptomic Diseases

24. ImAnno Gene List Output cadre sieves Cochlea Sacculus Utriculus url action Union Inter AnotB BnotA organ key action Union Inter AnotB BnotA Select Store EGEcoch EGEsac EGEutri EGEother action Union Inter AnotB BnotA Select Disease Jax Ihr Sanger All What to display name,descript,entrez,ege,go FromSieves UnionInter AnotBnotA GenePaintgenes UnionInter AnotBnotA HtmlTable FromStore

25. ImAnno Gene List

27. GxDb Uploading interface How to offer to the user an uploading tool allowing to combine experiments, arraytypes, samples, organisms, genotype, individuals, etc. using and connecting existing data, creating new one or updating it.

28. GxDb

30. GxDb Input Upload interface

31. Tricks and useful tools Store and Restore Works well as HTML form Allows to combine several pipeworks The user can create or extend Can be integrated in any.php page Can be called as a PHP function as function call as WebService

32. PipeWork ToDo list … Collapse parts Graphical interface Ajax requests Apply to other applications

33. Selector ! How to find the Experiments which were done with a given Organism and a set of Treatmentypes ? And for a Genotype and a Sample How to combine Experiments, RealExps, Sample, Arraytypes etc.

34. GxDb

35. … use Selector ! An application of the pipeworks MultipleSelectFromListOf

36. Selector … select from left to right Select one or more lines in a column Press the orange button to update the connected columns right from here Go to the next column When all is updated press the big orange button

37. 5 => 60, 61, 62 => 27, 28 and 11

38. 11 => 5, 34, 37 (hourrah 5 is present ! )

39. GxDb

40. Find the way …

41. Selector and PipeWork A Selector can contain PipeWorks (it is a PipeWork with special properties) Select, Press And press the output button to process A Selector can not yet be embedded in a PipeWork ??

42. Selector ToDo list … Graphical interface … any idea ? Customisable in size and display Ajax Apply to other applications Test it outside Genoret or Gx require_once, etc.

43. Merci à Laëtitia Nicolas Guillaume