BioExtract Server
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The BioExtract Server (bioextract.org), funded by the United States National Science Foundation, is a Web-based, workflow-enabling system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatics workflows. The BioExtract Server provides: 1) a flexible querying and retrieval interface to National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI) non-redundant nucleotide and protein databases, 2) the ability to filter query results and use them as input into analytic tools, 3) the facility to save query results as data extracts which are automatically integrated into the system as searchable data sets, 4) access to analytic tools including a large list of curated Web services such as Emboss (http://www.ebi.ac.uk/Tools/emboss/) and BioMart (http://www.biomart.org/) resources, 5) the ability to save a series of BioExtract Server tasks (e.g. query a data source, save a data extract and execute an analytic tool) as a workflow, and 6) the opportunity for researchers to share their data extracts, analytic tools and workflows with collaborators.
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BioExtract Server
- 1. 7/24/2013 Carol M. Lushbough Etienne Z. Gnimpieba Rion Dooley Contact: Carol.Lushbough@usd.edu
- 2. Overview of the iPlant Discovery Environment • http://www.iplantcollaborative.org/discover/discovery- environment 7/24/2013
- 4. 7/24/2013
- 5. Login to iPlant Discovery Environment 7/24/2013
- 9. Bulk Upload from Desktop 7/24/2013
- 10. Uploaded iPlant Data File Sample Upload File to iPlant Discovery Environment File Size ~2.27 G Queue Time ~3 minutes Transfer time ~36 minutes 7/24/2013
- 11. View iPlant Data File 7/24/2013
- 12. Overview of the iPlant Foundation API • http://iplant-dev.tacc.utexas.edu/v1/foundation-backbone 7/24/2013
- 13. Overview of the iPlant Foundation API • Enter you iPlant username and password and click Get Token 7/24/2013
- 14. iPlant Foundation API Authentication 7/24/2013
- 15. iPlant Foundation API Browse Files 7/24/2013
- 16. iPlant Foundation API Input/Output 7/24/2013
- 17. iPlant Foundation API Applications 7/24/2013
- 18. iPlant Foundation API APPS Discovery Endpoints 7/24/2013
- 19. iPlant Foundation API APPS Management Endpoints 7/24/2013
- 20. iPlant Foundation API JOB 7/24/2013
- 21. BioExtract Server • Query multiple data sources • Export search results • Save search results as searchable data extracts • Execute distributed analytic tools • Create, execute, modify, report, and share workflows 7/24/2013
- 23. Registering with the BioExtract Server 7/24/2013
- 24. BioExtract Server Data Query 7/24/2013
- 25. Creating a Query 7/24/2013 1. Select UniProtKB. 2. Use the Search Field drop-down menu and select Gene. 3. In the Search Term box, type myb*. 4. Click the Add Search Line button to add an additional search expression. Boolean search expression options are AND, OR, AND NOT. For our example, select AND. 5. From the Search Field drop-down menu, select Taxonomy. 6. In the Search Term box, type in Panicoideae. 7. Click Submit Query button. Query results will display under the “Extracts” tab.
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- 31. Analytic Tool Availability • Access the set of commonly used analytic tools that have been incorporated into the system including iPlant tools available through the iPlant Foundation API
- 32. Analyzing Data within the BioExtract Server 7/24/2013 The basic steps for executing tools are: Step 1. Select a tool Step 2. Input some data Step 3. Define parameters Step 4. Click Execute and wait Step 5. View tool results
- 33. Input Options
- 34. Executing an Analytic Tool 7/24/2013 1. Select blastn from the list of Similarity Search Tools in the Tools list 2. Select the Paste or type data into the text area radio button 3. Enter: XM_001061943 4. Click the Execute button
- 35. Executing an Analytic Tool 7/24/2013
- 38. Execution Results Saved at iPlant 7/24/2013
- 39. Data Extract from BLASTN Execution 7/24/2013
- 42. Use File Stored at iPlant as Input into Analytic Tool 7/24/2013
- 43. BioExtract Server Workflows 7/24/2013 • As the researcher works with the system, their tasks or “steps” are saved in the background. • At any time these steps can be saved as a workflow simply by providing a name and description. • Once saved, these workflows can be executed and/or modified.
- 44. Preparing to Record a Workflow 7/24/2013
- 45. Creating a Workflow 7/24/2013 1. Find all protein sequences that relate to the FXN gene in humans but excluding the full sequence. 2. Save the result set. 3. Execute the EMBOSS showalign analytic tool to align the resulting sequence record. 4. Execute NCBI BLASTP to find similar sequences from the swissprot database. 5. Execute TCoffee to perform a multiple sequence alignment of the similar sequences. 6. Execute iPlant’s Muscle to perform another multiple seqeunces alignment for comparison. 7. Finally, perform a multiple sequence alignment using iPlant’s Clustal Omega using the results from the TCoffee alignment.
- 46. Find all protein sequences that relate to the FXN gene in humans but excluding the full sequence. 7/24/2013
- 47. 7/24/2013
- 48. Save the result set 7/24/2013
- 49. Created a Searchable Data Extract 7/24/2013
- 50. Execute the EMBOSS showalign analytic tool to align the resulting sequence record. 7/24/2013
- 51. View Show Align Results 7/24/2013
- 52. View Show Align Results 7/24/2013
- 53. BLASTP Input – Current Extract 7/24/2013
- 54. Execute NCBI BLASTP to find similar sequences from the swissprot database 7/24/2013
- 57. Execute TCoffee to perform a multiple sequence alignment of the similar sequences 7/24/2013
- 59. Save TCoffee Results at iPlant 7/24/2013
- 60. Execute iPlant’s Muscle to perform another multiple sequences alignment for comparison 7/24/2013
- 62. Execute iPlant’s Clustal Omega to perform another multiple sequences alignment for comparison 7/24/2013
- 67. 7/24/2013
- 68. Modifying a Workflow 7/24/2013 Modify the query to search for the wcaG gene in Salmonella Typhimurium common:gene=wcaG AND common:species=Salmonella AND common:defn='Typhimurium' GUI Search Field Common search fields All Text common:all Id common:id Author common: author Title common: title Accession common: accn Definition common: defn Feature Key common: fkey Gene common: gene Keywords common: keyword Species common: species
- 69. Modify Query within Workflow 7/24/2013
- 70. Modify Analytic Tool Parameter 7/24/2013
- 71. The myexperiment.org social web site, launched in November 2007 myExperiment is a collaborative environment where scientists can safely publish their workflows and experiment plans, share them with groups and find those of others. myExperiment is brought to you by a joint team from the University of Southampton and The University of Manchester in the UK, led by David De Roure and Carole Goble,
- 76. Acknowledgements Volker Brendel - Professor of Biology and Computer Science at Indiana University in Bloomington. Rion Dooley – Manager, Web & Cloud Services Group, Texas Advanced Computing Center. iPlant Collaborative - This work was created using resources or cyberinfrastructure provided by the iPlant Collaborative. The iPlant Collaborative is funded by a grant from the National Science Foundation (#DBI- 0735191). URL: www.iplantcollaborative.org Funded through NSF IOS-1126481 NSF Plant Genome Research National Science Foundation