7/24/2013
Carol M. Lushbough
Etienne Z. Gnimpieba
Rion Dooley
Contact: Carol.Lushbough@usd.edu
Overview of the iPlant Discovery
Environment
• http://www.iplantcollaborative.org/discover/discovery-
environment
7/24/2013
Register
7/24/2013
7/24/2013
Login to iPlant Discovery Environment
7/24/2013
iPlant Data
7/24/2013
iPlant Data Options
7/24/2013
iPlant File Upload
7/24/2013
Bulk Upload from Desktop
7/24/2013
Uploaded iPlant Data File
Sample Upload File to iPlant Discovery Environment
File Size ~2.27 G
Queue Time ~3 minutes
Trans...
View iPlant Data File
7/24/2013
Overview of the iPlant Foundation API
• http://iplant-dev.tacc.utexas.edu/v1/foundation-backbone
7/24/2013
Overview of the iPlant Foundation API
• Enter you iPlant username and password and click Get
Token
7/24/2013
iPlant Foundation API Authentication
7/24/2013
iPlant Foundation API Browse Files
7/24/2013
iPlant Foundation API Input/Output
7/24/2013
iPlant Foundation API Applications
7/24/2013
iPlant Foundation API APPS Discovery
Endpoints
7/24/2013
iPlant Foundation API APPS Management
Endpoints
7/24/2013
iPlant Foundation API JOB
7/24/2013
BioExtract Server
• Query multiple data sources
• Export search results
• Save search results as searchable data
extracts
...
BioExtract Server
7/24/2013
Registering with the BioExtract Server
7/24/2013
BioExtract Server Data Query
7/24/2013
Creating a Query
7/24/2013
1. Select UniProtKB.
2. Use the Search Field drop-down menu and select Gene.
3. In the Search T...
7/24/2013
Data Extracts
7/24/2013
Saving Data Extracts
7/24/2013
Query Data Extract
7/24/2013
7/24/2013
Analytic Tool Availability
• Access the set of commonly used analytic tools that have
been incorporated into the system in...
Analyzing Data within the BioExtract
Server
7/24/2013
The basic steps for executing
tools are:
Step 1. Select a tool
Step ...
Input Options
Executing an Analytic Tool
7/24/2013
1. Select blastn from the list of Similarity Search Tools in the Tools list
2. Select...
Executing an Analytic Tool
7/24/2013
View Execution Results
7/24/2013
Saving Execution Results
7/24/2013
Execution Results Saved at iPlant
7/24/2013
Data Extract from BLASTN Execution
7/24/2013
iPlant Collaborative Tools
7/24/2013
iPlant Collaborative Tools
7/24/2013
Use File Stored at iPlant as Input into
Analytic Tool
7/24/2013
BioExtract Server Workflows
7/24/2013
• As the researcher works with the system, their
tasks or “steps” are saved in the b...
Preparing to Record a Workflow
7/24/2013
Creating a Workflow
7/24/2013
1. Find all protein sequences that relate to the FXN gene in humans but
excluding the full s...
Find all protein sequences that relate to the FXN gene in
humans but excluding the full sequence.
7/24/2013
7/24/2013
Save the result set
7/24/2013
Created a Searchable Data Extract
7/24/2013
Execute the EMBOSS showalign analytic tool to align
the resulting sequence record.
7/24/2013
View Show Align Results
7/24/2013
View Show Align Results
7/24/2013
BLASTP Input – Current Extract
7/24/2013
Execute NCBI BLASTP to find similar sequences from
the swissprot database
7/24/2013
BLASTP Results
7/24/2013
BLASTP Results
7/24/2013
Execute TCoffee to perform a multiple sequence
alignment of the similar sequences
7/24/2013
TCoffee Results
7/24/2013
Save TCoffee Results at iPlant
7/24/2013
Execute iPlant’s Muscle to perform another multiple
sequences alignment for comparison
7/24/2013
iPlant’s Muscle Results
7/24/2013
Execute iPlant’s Clustal Omega to perform another
multiple sequences alignment for comparison
7/24/2013
Clustal Omega Results
7/24/2013
Saving a Workflow
7/24/2013
Executing a Workflow
7/24/2013
Viewing Executed Process
7/24/2013
7/24/2013
Modifying a Workflow
7/24/2013
Modify the query to search for the wcaG gene in Salmonella Typhimurium
common:gene=wcaG AND...
Modify Query within Workflow
7/24/2013
Modify Analytic Tool Parameter
7/24/2013
The myexperiment.org social web site, launched in
November 2007
myExperiment is a collaborative environment where
scientis...
Modify input
Modify Input
Acknowledgements
 Volker Brendel - Professor of Biology and Computer
Science at Indiana University in Bloomington.
 Rion...
BioExtract Server
BioExtract Server
BioExtract Server
Upcoming SlideShare
Loading in …5
×

BioExtract Server

411 views

Published on

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.

Published in: Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
411
On SlideShare
0
From Embeds
0
Number of Embeds
1
Actions
Shares
0
Downloads
3
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

BioExtract Server

  1. 1. 7/24/2013 Carol M. Lushbough Etienne Z. Gnimpieba Rion Dooley Contact: Carol.Lushbough@usd.edu
  2. 2. Overview of the iPlant Discovery Environment • http://www.iplantcollaborative.org/discover/discovery- environment 7/24/2013
  3. 3. Register 7/24/2013
  4. 4. 7/24/2013
  5. 5. Login to iPlant Discovery Environment 7/24/2013
  6. 6. iPlant Data 7/24/2013
  7. 7. iPlant Data Options 7/24/2013
  8. 8. iPlant File Upload 7/24/2013
  9. 9. Bulk Upload from Desktop 7/24/2013
  10. 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. 11. View iPlant Data File 7/24/2013
  12. 12. Overview of the iPlant Foundation API • http://iplant-dev.tacc.utexas.edu/v1/foundation-backbone 7/24/2013
  13. 13. Overview of the iPlant Foundation API • Enter you iPlant username and password and click Get Token 7/24/2013
  14. 14. iPlant Foundation API Authentication 7/24/2013
  15. 15. iPlant Foundation API Browse Files 7/24/2013
  16. 16. iPlant Foundation API Input/Output 7/24/2013
  17. 17. iPlant Foundation API Applications 7/24/2013
  18. 18. iPlant Foundation API APPS Discovery Endpoints 7/24/2013
  19. 19. iPlant Foundation API APPS Management Endpoints 7/24/2013
  20. 20. iPlant Foundation API JOB 7/24/2013
  21. 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
  22. 22. BioExtract Server 7/24/2013
  23. 23. Registering with the BioExtract Server 7/24/2013
  24. 24. BioExtract Server Data Query 7/24/2013
  25. 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.
  26. 26. 7/24/2013
  27. 27. Data Extracts 7/24/2013
  28. 28. Saving Data Extracts 7/24/2013
  29. 29. Query Data Extract 7/24/2013
  30. 30. 7/24/2013
  31. 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. 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. 33. Input Options
  34. 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. 35. Executing an Analytic Tool 7/24/2013
  36. 36. View Execution Results 7/24/2013
  37. 37. Saving Execution Results 7/24/2013
  38. 38. Execution Results Saved at iPlant 7/24/2013
  39. 39. Data Extract from BLASTN Execution 7/24/2013
  40. 40. iPlant Collaborative Tools 7/24/2013
  41. 41. iPlant Collaborative Tools 7/24/2013
  42. 42. Use File Stored at iPlant as Input into Analytic Tool 7/24/2013
  43. 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. 44. Preparing to Record a Workflow 7/24/2013
  45. 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. 46. Find all protein sequences that relate to the FXN gene in humans but excluding the full sequence. 7/24/2013
  47. 47. 7/24/2013
  48. 48. Save the result set 7/24/2013
  49. 49. Created a Searchable Data Extract 7/24/2013
  50. 50. Execute the EMBOSS showalign analytic tool to align the resulting sequence record. 7/24/2013
  51. 51. View Show Align Results 7/24/2013
  52. 52. View Show Align Results 7/24/2013
  53. 53. BLASTP Input – Current Extract 7/24/2013
  54. 54. Execute NCBI BLASTP to find similar sequences from the swissprot database 7/24/2013
  55. 55. BLASTP Results 7/24/2013
  56. 56. BLASTP Results 7/24/2013
  57. 57. Execute TCoffee to perform a multiple sequence alignment of the similar sequences 7/24/2013
  58. 58. TCoffee Results 7/24/2013
  59. 59. Save TCoffee Results at iPlant 7/24/2013
  60. 60. Execute iPlant’s Muscle to perform another multiple sequences alignment for comparison 7/24/2013
  61. 61. iPlant’s Muscle Results 7/24/2013
  62. 62. Execute iPlant’s Clustal Omega to perform another multiple sequences alignment for comparison 7/24/2013
  63. 63. Clustal Omega Results 7/24/2013
  64. 64. Saving a Workflow 7/24/2013
  65. 65. Executing a Workflow 7/24/2013
  66. 66. Viewing Executed Process 7/24/2013
  67. 67. 7/24/2013
  68. 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. 69. Modify Query within Workflow 7/24/2013
  70. 70. Modify Analytic Tool Parameter 7/24/2013
  71. 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,
  72. 72. Modify input Modify Input
  73. 73. 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

×