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PipeWork and Selector

PipeWork and Selector. Raymond Ripp. Output. A simple PipeWork : Calculette. Add. Output. Output. Enter the values and press. 5. 4. Add. = 9. Output. Predefined inputs. 5. Add. Output. Edit the PipeWork. Multiply. Add. Output. Processing Elements.

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PipeWork and Selector

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  1. PipeWork and Selector Raymond Ripp

  2. Output A simple PipeWork : Calculette Add

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

  4. Output Predefined inputs 5 Add

  5. Output Edit the PipeWork Multiply Add

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

  7. 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 Processing Elements 1/6

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

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

  10. 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. Processing Elements 4/6

  11. 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 Processing Elements 5/6

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

  17. Create Edit Manage PipeWorks

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

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

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

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

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

  25. ImAnno Gene List

  26. 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.

  27. GxDb

  28. GxDb Input Upload interface

  29. 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

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

  31. 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.

  32. GxDb

  33. … use Selector ! An application of the pipework’s MultipleSelectFromListOf

  34. 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

  35. 5 => 60, 61, 62 => 27, 28 and 11

  36. 11 => 5, 34, 37 (hourrah 5 is present ! )

  37. GxDb

  38. Find the way …

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

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

  41. Merci à • Laëtitia • Nicolas • Guillaume

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