Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

2014 Taverna Tutorial Components

534 views

Published on

2014-09-01 Taverna tutorial in Bonn: Components as a mechanism to package and reuse workflow fragments.

Published in: Software
  • Writing good research paper is quite easy and very difficult simultaneously. It depends on the individual skill set also. You can get help from research paper writing. Check out, please ⇒ www.HelpWriting.net ⇐
       Reply 
    Are you sure you want to  Yes  No
    Your message goes here
  • D0WNL0AD FULL ▶ ▶ ▶ ▶ http://1lite.top/SGaI0 ◀ ◀ ◀ ◀
       Reply 
    Are you sure you want to  Yes  No
    Your message goes here
  • ⇒ www.WritePaper.info ⇐ is a good website if you’re looking to get your essay written for you. You can also request things like research papers or dissertations. It’s really convenient and helpful.
       Reply 
    Are you sure you want to  Yes  No
    Your message goes here
  • DOWNLOAD THIS BOOKS INTO AVAILABLE FORMAT (2019 Update) ......................................................................................................................... ......................................................................................................................... Download Full PDF EBOOK here { https://soo.gd/irt2 } ......................................................................................................................... Download Full EPUB Ebook here { https://soo.gd/irt2 } ......................................................................................................................... Download Full doc Ebook here { https://soo.gd/irt2 } ......................................................................................................................... Download PDF EBOOK here { https://soo.gd/irt2 } ......................................................................................................................... Download EPUB Ebook here { https://soo.gd/irt2 } ......................................................................................................................... Download doc Ebook here { https://soo.gd/irt2 } ......................................................................................................................... ......................................................................................................................... ................................................................................................................................... eBook is an electronic version of a traditional print book THIS can be read by using a personal computer or by using an eBook reader. (An eBook reader can be a software application for use on a computer such as Microsoft's free Reader application, or a book-sized computer THIS is used solely as a reading device such as Nuvomedia's Rocket eBook.) Users can purchase an eBook on diskette or CD, but the most popular method of getting an eBook is to purchase a downloadable file of the eBook (or other reading material) from a Web site (such as Barnes and Noble) to be read from the user's computer or reading device. Generally, an eBook can be downloaded in five minutes or less ......................................................................................................................... .............. Browse by Genre Available eBooks .............................................................................................................................. Art, Biography, Business, Chick Lit, Children's, Christian, Classics, Comics, Contemporary, Cookbooks, Manga, Memoir, Music, Mystery, Non Fiction, Paranormal, Philosophy, Poetry, Psychology, Religion, Romance, Science, Science Fiction, Self Help, Suspense, Spirituality, Sports, Thriller, Travel, Young Adult, Crime, Ebooks, Fantasy, Fiction, Graphic Novels, Historical Fiction, History, Horror, Humor And Comedy, ......................................................................................................................... ......................................................................................................................... .....BEST SELLER FOR EBOOK RECOMMEND............................................................. ......................................................................................................................... Blowout: Corrupted Democracy, Rogue State Russia, and the Richest, Most Destructive Industry on Earth,-- The Ride of a Lifetime: Lessons Learned from 15 Years as CEO of the Walt Disney Company,-- Call Sign Chaos: Learning to Lead,-- StrengthsFinder 2.0,-- Stillness Is the Key,-- She Said: Breaking the Sexual Harassment Story THIS Helped Ignite a Movement,-- Atomic Habits: An Easy & Proven Way to Build Good Habits & Break Bad Ones,-- Everything Is Figureoutable,-- What It Takes: Lessons in the Pursuit of Excellence,-- Rich Dad Poor Dad: What the Rich Teach Their Kids About Money THIS the Poor and Middle Class Do Not!,-- The Total Money Makeover: Classic Edition: A Proven Plan for Financial Fitness,-- Shut Up and Listen!: Hard Business Truths THIS Will Help You Succeed, ......................................................................................................................... .........................................................................................................................
       Reply 
    Are you sure you want to  Yes  No
    Your message goes here
  • D0WNL0AD FULL ▶ ▶ ▶ ▶ http://1lite.top/SGaI0 ◀ ◀ ◀ ◀
       Reply 
    Are you sure you want to  Yes  No
    Your message goes here
  • Be the first to like this

2014 Taverna Tutorial Components

  1. 1. An Introduction to Taverna Components Stian Soiland-Reyes and Christian Brenninkmeijer University of Manchester materials by Aleksandra Pawlik http://orcid.org/0000-0001-9842-9718 http://orcid.org/0000-0002-2937-7819 http://orcid.org/0000-0002-1279-5133 http://orcid.org/0000-0001-8418-6735 Bonn University, 2014-09-01 http://www.taverna.org.uk/ This work is licensed under a Creative Commons Attribution 3.0 Unported License
  2. 2. • Something that can be put into a workflow • Well described - what the component does • Behaves “well” - conforms to agreed good practice • Curated - someone looks after it • Produces and consumes data in agreed formats • Fails in described ways - meaningful error messages • Produces agreed type of provenance • Documentation • Example usage
  3. 3. • Hide complexity • Predictable good behaviour • Guaranteed to work together • Can (in theory) check that data in a run conforms to the component specification
  4. 4. • The agreement is a condition of being in a “component family” • Different domains, or even different uses within a domain, have different agreements • Astronomical data is not in the same formats as biodiversity data • Digital library components do not do the same tasks as biodiversity components • Agreement is formalized as a “component profile”
  5. 5. • A component family is • a pack on myExperiment, or • a directory on your local machine • A component is defined by a workflow (in a pack) in a component family pack • Components are versioned by the myExperiment’s versioning • Semantic annotations are stored in RDF as part of the workflow definition • Collated semantics, including workflow structure, are combined on myExperiment.
  6. 6. • Contains: • Workflow ‘realizing’ the component • Example data • Documentation • Dependency specification
  7. 7. • A component family is shown in the service panel of Taverna workbench • Components can be included within a Taverna workflow • Components are not simply the same as nested workflows • You could think of them as nested workflows that obey a set of rules and where you cannot see what is nested (and should not care)
  8. 8. • Components are created by annotating a workflow • Choice of a component family and so profile • Semantic annotation from the specified ontologies • Validation against the profile • Component saved into the component family • Can annotate: • Workflow • Input/Output ports • Services inside workflow • Extensions to myExperiment for • Pack snapshots • Semantic collation • Semantic searching
  9. 9. • Use of components will allow • Component developers to work on the component • Component users to upgrade (or revert) the component versions • A workflow to remain ‘unchanged’ (if the component interfaces remain the same) • Powerful and dangerous • Proxies for components (re-run and re-play) • Components are “black boxes” in the workflow and workflow runs
  10. 10. EBI InterproScan  The workflow to call EBI InterproScan was quite complex.  It would be nice to be able to package that workflow up and be able to use it as a single service in other workflows  That is exactly what components allow
  11. 11. Importing a component family  Components are grouped into component families  Component families are held in a component registry  myExperiment is a component registry  You can import a component family into the Service Panel  Click Import new services and then  Component service…
  12. 12. Selecting a component family  In the dialog  Select myExperiment component registry, and  Test components family  Click OK
  13. 13. Added component family  In the Service panel you can now expand and see the Test components family
  14. 14. Adding a component to a workflow  Create a new workflow  Add the EBI_InterproScan component into the workflow  Create input and output workflow ports and connect them to the ports of the component
  15. 15. EBI InterproScan component
  16. 16. Running the workflow  You can now run the workflow  The value for the sequence should be something like: >sp|Q9BTV4|TMM43_HUMAN Transmembrane protein 43 OS=Homo sapiens GN=TMEM43 PE=1 SV=1 MAANYSSTSTRREHVKVKTSSQPGFLERLSETSGGMFVGLMAFLLSFYLIFTNEGRALKT ATSLAEGLSLVVSPDSIHSVAPENEGRLVHIIGALRTSKLLSDPNYGVHLPAVKLRRHVE MYQWVETEESREYTEDGQVKKETRYSYNTEWRSEIINSKNFDREIGHKNPSAMAVESFMA TAPFVQIGRFFLSSGLIDKVDNFKSLSLSKLEDPHVDIIRRGDFFYHSENPKYPEVGDLR VSFSYAGLSGDDPDLGPAHVVTVIARQRGDQLVPFSTKSGDTLLLLHHGDFSAEEVFHRE LRSNSMKTWGLRAAGWMAMFMGLNLMTRILYTLVDWFPVFRDLVNIGLKAFAFCVATSLT LLTVAAGWLFYRPLWALLIAGLALVPILVARTRVPAKKLE
  17. 17. Connecting components  The workflow just contains the single service, we need to connect the component with other services  In the Design view, delete the sequence workflow input port  Right click and select Delete workflow input port  Add Local Services -> ncbi -> Get Protein FASTA to the workflow  Connect the outputText of Get Protein FASTA to the sequence port of the EBI_InterproScan  Connect the id port of Get Protein FASTA to a workflow input port
  18. 18. Connected component Your workflow should now look like:
  19. 19. Running the workflow - 2  Run the workflow again  You can use Q9BTV4 as the value for id
  20. 20. Is it really the complex workflow?  In the Results view you can click on Progress report  Expand EBI_InterproScan  You can see all the services “hidden” inside the component
  21. 21.  The menu has a “Components” option  Select “Create family”
  22. 22.  In the pop-up window set the registry to local  Select a Profile (or see next slide if no profile available)  Enter the family name (“ProcessString”)
  23. 23.  Find your local registry directory  Hint: Components/ Manage Registries  Registry Location  In MyExperiment find the Empty profile  Hint: http://www.myexperiment.org/files/1027.html  Down File into the local registry directory
  24. 24.  Add a local service “Split string into string list by regular expression” (from ‘text’)  Add the input port and set the regular expression to space  Add a local service “Remove string duplicates” (from ‘list’)  Connect the output from “Split string into string list by regular expression” with the input of “Remove string duplicates”  Add a local service “Merge String List to a String” and connect its input with the “Remove string duplicates” output and set the separator to be a space
  25. 25.  Select “Create component” from the “Components” menu  Provide a name for the component (Remove duplicates)  You should see a pink ribbon at the top  Save the component. You will see a warning message – it pops up because the component is not annotated. We can annotate it in the component details.
  26. 26.  Close any open workflows  Add the component(s) to the service panel  Hint: Import Service/ Component Family  Component registry: Local registry  Component family: ProcessString  Add the component to the workflow  Hint: Available services/ Components …  Add input and output ports  Run

×