MyDasty

 Omar Pera

Background


                 Presentation of the project:
Objetives

Features
                      ...
Outline of the presentation

  MyDasty

 Omar Pera

Background

                     Background
Objetives

Features
      ...
Background
                 Dasty2

  MyDasty

 Omar Pera
                  Dasty2 is a powerful web client for visualizin...
Background
                 Dasty2 process

  MyDasty

                  The general process that takes Dasty2 to visualiz...
Background
                 Dasty2 process

  MyDasty

                  The general process that takes Dasty2 to visualiz...
Background
                 Dasty2 process

  MyDasty

                  The general process that takes Dasty2 to visualiz...
Background
                 Dasty2 process

  MyDasty

                  The general process that takes Dasty2 to visualiz...
Background
                 Dasty2 process

  MyDasty

                  The general process that takes Dasty2 to visualiz...
Background
                 Dasty2 search page

  MyDasty

 Omar Pera

Background

Objetives
                   Main page ...
MyDasty

 Omar Pera

Background

Objetives

Features

User
                 How to improve this search page?
configuration
...
MyDasty

 Omar Pera

Background

Objetives

Features

User
                 How to improve this search page?
configuration
...
MyDasty

  MyDasty

 Omar Pera

Background

Objetives

Features

User
configuration
                  It is an extension of...
Objectives

  MyDasty

 Omar Pera

Background

                     Let users have more control over the search before
Obj...
Features

   MyDasty

 Omar Pera

Background
                        In order to achieve this objectives we proposed sever...
Features

   MyDasty

 Omar Pera

Background
                        In order to achieve this objectives we proposed sever...
Features

   MyDasty

 Omar Pera

Background
                        In order to achieve this objectives we proposed sever...
Features

   MyDasty

 Omar Pera

Background
                        In order to achieve this objectives we proposed sever...
Selection of DAS sources
                        Context

   MyDasty

 Omar Pera

Background

                            ...
Selection of DAS sources

   MyDasty

 Omar Pera

Background

                        We will use DAS registry to allow th...
Selection of DAS sources

   MyDasty

 Omar Pera

Background

                        We will use DAS registry to allow th...
Selection of DAS sources

   MyDasty

 Omar Pera

Background

                        We will use DAS registry to allow th...
Selection of DAS sources

   MyDasty

 Omar Pera

Background

                        We will use DAS registry to allow th...
Filtering features by type and category
                        Context

   MyDasty

 Omar Pera

Background

Objetives

Fe...
Filtering features by type and category

   MyDasty

 Omar Pera

Background

                        The main objective of...
Mapping protein accessions from other
                        databases
                        Context
   MyDasty

 Omar ...
Mapping protein accessions from other
                        databases
   MyDasty

 Omar Pera

Background

Objetives

   ...
Mapping protein accessions from other
                        databases
   MyDasty

 Omar Pera

Background

Objetives

   ...
Mapping protein accessions from other
                        databases
   MyDasty

 Omar Pera

Background

Objetives

   ...
Mapping protein accessions from other
                        databases
   MyDasty

 Omar Pera

Background
               ...
User configuration

  MyDasty

 Omar Pera

Background

Objetives

Features

User
                     We need to solve the ...
User configuration

  MyDasty

 Omar Pera

Background

                 We have to consider two types of users on the syste...
User configuration

  MyDasty

 Omar Pera

Background

                 We have to consider two types of users on the syste...
User configuration

  MyDasty

 Omar Pera

Background

                 We have to consider two types of users on the syste...
User configuration
                 Registered users

  MyDasty

 Omar Pera

Background

Objetives

Features
              ...
User configuration
                 Registered users

  MyDasty

 Omar Pera

Background

Objetives

Features
              ...
User configuration
                 OpenID

  MyDasty

 Omar Pera

Background
                   It is a shared identity se...
User configuration
                 OpenID

  MyDasty

 Omar Pera

Background

Objetives

                      The necessi...
User configuration
                 OpenID

  MyDasty

 Omar Pera

Background

Objetives

                      The necessi...
User configuration
                 OpenID

  MyDasty

 Omar Pera

Background

Objetives

                      The necessi...
Storage system

  MyDasty

 Omar Pera

Background

Objetives

Features

User
                 In order to save the configur...
Storage system

  MyDasty

 Omar Pera

Background
                    We will give the option to choose about the followin...
Storage system

  MyDasty

 Omar Pera

Background
                    We will give the option to choose about the followin...
Storage system

  MyDasty

 Omar Pera

Background
                    We will give the option to choose about the followin...
Storage system

  MyDasty

 Omar Pera

Background
                    We will give the option to choose about the followin...
Technologies in use

  MyDasty

 Omar Pera

Background

Objetives
                 Server:
Features
                     P...
Extra possible features

  MyDasty

 Omar Pera
                     Allow to configure the layout of Dasty2 as well as the
...
MyDasty

 Omar Pera

Background

Objetives

Features

User
configuration

                 Any question, suggestion, idea ?...
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MyDasty, advanced search page for Dasty2

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MyDasty is an extension of the search page of Dasty2 that let users have more control over the search, facilitate users to configure Dasty2 and give the option to save and restore their configuration.

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MyDasty, advanced search page for Dasty2

  1. 1. MyDasty Omar Pera Background Presentation of the project: Objetives Features MyDasty User configuration Storage system Omar Pera Mira Technologies in use Extra possible European Bioinformatics Institute features July 24, 2008
  2. 2. Outline of the presentation MyDasty Omar Pera Background Background Objetives Features Objectives User configuration Features Storage User configuration system Technologies Storage system in use Technologies in use Extra possible features Extra features
  3. 3. Background Dasty2 MyDasty Omar Pera Dasty2 is a powerful web client for visualizing protein Background sequence features using the DAS protocol. Objetives Features User configuration Storage system Technologies in use Extra possible features
  4. 4. Background Dasty2 process MyDasty The general process that takes Dasty2 to visualize protein Omar Pera sequence information is: Background The client establishes an initial connection to the DAS Objetives Features Registry and retrieves a list of available DAS User annotation servers. configuration Connects to the Uniprot DAS reference server and Storage system retrieves sequence information. Technologies in use It accepts Uniprot accession numbers or Uniprot ID’s. Extra possible features Retrieves feature information from one or more DAS annotation servers filtered by label. Merges the collected data and provides the user with a view of the sequence and its annotated features.
  5. 5. Background Dasty2 process MyDasty The general process that takes Dasty2 to visualize protein Omar Pera sequence information is: Background The client establishes an initial connection to the DAS Objetives Features Registry and retrieves a list of available DAS User annotation servers. configuration Connects to the Uniprot DAS reference server and Storage system retrieves sequence information. Technologies in use It accepts Uniprot accession numbers or Uniprot ID’s. Extra possible features Retrieves feature information from one or more DAS annotation servers filtered by label. Merges the collected data and provides the user with a view of the sequence and its annotated features.
  6. 6. Background Dasty2 process MyDasty The general process that takes Dasty2 to visualize protein Omar Pera sequence information is: Background The client establishes an initial connection to the DAS Objetives Features Registry and retrieves a list of available DAS User annotation servers. configuration Connects to the Uniprot DAS reference server and Storage system retrieves sequence information. Technologies in use It accepts Uniprot accession numbers or Uniprot ID’s. Extra possible features Retrieves feature information from one or more DAS annotation servers filtered by label. Merges the collected data and provides the user with a view of the sequence and its annotated features.
  7. 7. Background Dasty2 process MyDasty The general process that takes Dasty2 to visualize protein Omar Pera sequence information is: Background The client establishes an initial connection to the DAS Objetives Features Registry and retrieves a list of available DAS User annotation servers. configuration Connects to the Uniprot DAS reference server and Storage system retrieves sequence information. Technologies in use It accepts Uniprot accession numbers or Uniprot ID’s. Extra possible features Retrieves feature information from one or more DAS annotation servers filtered by label. Merges the collected data and provides the user with a view of the sequence and its annotated features.
  8. 8. Background Dasty2 process MyDasty The general process that takes Dasty2 to visualize protein Omar Pera sequence information is: Background The client establishes an initial connection to the DAS Objetives Features Registry and retrieves a list of available DAS User annotation servers. configuration Connects to the Uniprot DAS reference server and Storage system retrieves sequence information. Technologies in use It accepts Uniprot accession numbers or Uniprot ID’s. Extra possible features Retrieves feature information from one or more DAS annotation servers filtered by label. Merges the collected data and provides the user with a view of the sequence and its annotated features.
  9. 9. Background Dasty2 search page MyDasty Omar Pera Background Objetives Main page which retrieves a Protein Accession number or Features ID and executes Dasty. User configuration Storage system Technologies in use Extra possible features
  10. 10. MyDasty Omar Pera Background Objetives Features User How to improve this search page? configuration Storage MyDasty system Technologies in use Extra possible features
  11. 11. MyDasty Omar Pera Background Objetives Features User How to improve this search page? configuration Storage MyDasty system Technologies in use Extra possible features
  12. 12. MyDasty MyDasty Omar Pera Background Objetives Features User configuration It is an extension of the search page that makes Dasty2 a Storage more configurable and powerful application. system Technologies in use Extra possible features
  13. 13. Objectives MyDasty Omar Pera Background Let users have more control over the search before Objetives the client starts. Features User Facilitate users to configure Dasty2 with their own configuration requirements. Storage system Give the option to save and restore the configuration Technologies done on MyDasty. in use Extra possible Improve Dasty2 with extra features such as not only features accept Uniprot accession numbers or ID’s.
  14. 14. Features MyDasty Omar Pera Background In order to achieve this objectives we proposed several Objetives features: Features Selection of DAS Full control about which DAS servers Dasty2 retrieves sources Filtering features by type and category protein annotations from. Mapping protein accessions from other databases Pre-configure Dasty2 to just display features of a User certain type or category. configuration Storage Mapping protein accessions from other databases (IPI, system ENSEMBL, etc.) to Uniprot accession. Technologies in use Extra possible features
  15. 15. Features MyDasty Omar Pera Background In order to achieve this objectives we proposed several Objetives features: Features Selection of DAS Full control about which DAS servers Dasty2 retrieves sources Filtering features by type and category protein annotations from. Mapping protein accessions from other databases Pre-configure Dasty2 to just display features of a User certain type or category. configuration Storage Mapping protein accessions from other databases (IPI, system ENSEMBL, etc.) to Uniprot accession. Technologies in use Extra possible features
  16. 16. Features MyDasty Omar Pera Background In order to achieve this objectives we proposed several Objetives features: Features Selection of DAS Full control about which DAS servers Dasty2 retrieves sources Filtering features by type and category protein annotations from. Mapping protein accessions from other databases Pre-configure Dasty2 to just display features of a User certain type or category. configuration Storage Mapping protein accessions from other databases (IPI, system ENSEMBL, etc.) to Uniprot accession. Technologies in use Extra possible features
  17. 17. Features MyDasty Omar Pera Background In order to achieve this objectives we proposed several Objetives features: Features Selection of DAS Full control about which DAS servers Dasty2 retrieves sources Filtering features by type and category protein annotations from. Mapping protein accessions from other databases Pre-configure Dasty2 to just display features of a User certain type or category. configuration Storage Mapping protein accessions from other databases (IPI, system ENSEMBL, etc.) to Uniprot accession. Technologies in use Extra possible features
  18. 18. Selection of DAS sources Context MyDasty Omar Pera Background By default, Dasty2 retrieves Objetives features filtered by Features Selection of DAS Biosapiens label. sources Filtering features by type and category There is no possibility to Mapping protein accessions from other databases display features from User private DAS servers. configuration Storage There are more than 60 system DAS servers that contain Technologies in use protein annotations. Extra possible features
  19. 19. Selection of DAS sources MyDasty Omar Pera Background We will use DAS registry to allow the user: Objetives Features Select from which DAS servers you want to retrieve Selection of DAS sources annotations. Filtering features by type and category Mapping protein Display features from private or test DAS servers giving accessions from other databases the URL. User configuration Possibility to display specific DAS sources first on the Storage graphic. system Technologies in use Extra possible features
  20. 20. Selection of DAS sources MyDasty Omar Pera Background We will use DAS registry to allow the user: Objetives Features Select from which DAS servers you want to retrieve Selection of DAS sources annotations. Filtering features by type and category Mapping protein Display features from private or test DAS servers giving accessions from other databases the URL. User configuration Possibility to display specific DAS sources first on the Storage graphic. system Technologies in use Extra possible features
  21. 21. Selection of DAS sources MyDasty Omar Pera Background We will use DAS registry to allow the user: Objetives Features Select from which DAS servers you want to retrieve Selection of DAS sources annotations. Filtering features by type and category Mapping protein Display features from private or test DAS servers giving accessions from other databases the URL. User configuration Possibility to display specific DAS sources first on the Storage graphic. system Technologies in use Extra possible features
  22. 22. Selection of DAS sources MyDasty Omar Pera Background We will use DAS registry to allow the user: Objetives Features Select from which DAS servers you want to retrieve Selection of DAS sources annotations. Filtering features by type and category Mapping protein Display features from private or test DAS servers giving accessions from other databases the URL. User configuration Possibility to display specific DAS sources first on the Storage graphic. system Technologies in use Extra possible features
  23. 23. Filtering features by type and category Context MyDasty Omar Pera Background Objetives Features Biosapiens Ontologies has provided an effective way Selection of DAS sources Filtering features by of structuring feature annotation. type and category Mapping protein accessions from Dasty2 already gives the option to filter protein features other databases by Biosapiens ontologies. User configuration Storage system Technologies in use Extra possible features
  24. 24. Filtering features by type and category MyDasty Omar Pera Background The main objective of this feature is allow the user to allow Objetives configure a more accurate search before the client Features Selection of DAS starts: sources Filtering features by type and category Mapping protein We will use Biosapiens Ontologies to display only accessions from other databases specific features filtered by: User configuration Type Storage Category system Technologies in use Extra possible features
  25. 25. Mapping protein accessions from other databases Context MyDasty Omar Pera Background Dasty2 only accepts Uniprot accession numbers or Objetives Uniprot ID’s. Features Selection of DAS sources When you request features or structural data from a Filtering features by type and category protein ID, it could happen that some information only Mapping protein accessions from other databases maps to his protein accession number. User configuration Protein Identifier Cross-Reference service ( PICR ) Storage is a tool capable to map protein identifiers to a large list system of databases. Technologies in use Extra possible features
  26. 26. Mapping protein accessions from other databases MyDasty Omar Pera Background Objetives We will use PICR to: Features Selection of DAS sources Map Uniprot protein ID’s to protein accession number. Filtering features by type and category Mapping from different source databases such as IPI, Mapping protein accessions from other databases Ensembl, TrEMBL or PIR to Uniprot protein accession User number, extending the possibilities of Dasty2 configuration Storage system Technologies in use Extra possible features
  27. 27. Mapping protein accessions from other databases MyDasty Omar Pera Background Objetives We will use PICR to: Features Selection of DAS sources Map Uniprot protein ID’s to protein accession number. Filtering features by type and category Mapping from different source databases such as IPI, Mapping protein accessions from other databases Ensembl, TrEMBL or PIR to Uniprot protein accession User number, extending the possibilities of Dasty2 configuration Storage system Technologies in use Extra possible features
  28. 28. Mapping protein accessions from other databases MyDasty Omar Pera Background Objetives We will use PICR to: Features Selection of DAS sources Map Uniprot protein ID’s to protein accession number. Filtering features by type and category Mapping from different source databases such as IPI, Mapping protein accessions from other databases Ensembl, TrEMBL or PIR to Uniprot protein accession User number, extending the possibilities of Dasty2 configuration Storage system Technologies in use Extra possible features
  29. 29. Mapping protein accessions from other databases MyDasty Omar Pera Background We will use PICR to: Objetives Map Uniprot protein ID’s to protein accession number. Features Selection of DAS sources Mapping from different source databases such as IPI, Filtering features by type and category Ensembl, TrEMBL or PIR to Uniprot protein accession Mapping protein accessions from number, extending the possibilities of Dasty2 other databases User configuration Storage system Technologies in use Extra possible features
  30. 30. User configuration MyDasty Omar Pera Background Objetives Features User We need to solve the problem of configuring the configuration parameters of MyDasty each time we want to run Storage system Dasty2. Technologies in use Extra possible features
  31. 31. User configuration MyDasty Omar Pera Background We have to consider two types of users on the system: Objetives Features Anonymous: Users who don’t want to retrieve their User configuration configuration in another time. Storage Registered: They are users who want to save his system configuration on the server. It means that all Technologies in use the parameters configured on myDasty could Extra possible be restored in the future. features
  32. 32. User configuration MyDasty Omar Pera Background We have to consider two types of users on the system: Objetives Features Anonymous: Users who don’t want to retrieve their User configuration configuration in another time. Storage Registered: They are users who want to save his system configuration on the server. It means that all Technologies in use the parameters configured on myDasty could Extra possible be restored in the future. features
  33. 33. User configuration MyDasty Omar Pera Background We have to consider two types of users on the system: Objetives Features Anonymous: Users who don’t want to retrieve their User configuration configuration in another time. Storage Registered: They are users who want to save his system configuration on the server. It means that all Technologies in use the parameters configured on myDasty could Extra possible be restored in the future. features
  34. 34. User configuration Registered users MyDasty Omar Pera Background Objetives Features There is a neeed of an account with user/pass for each User user who wants to save his configuration. configuration Storage It is more reasonable for this project to take advantage system of the possibilities of OpenID. Technologies in use Extra possible features
  35. 35. User configuration Registered users MyDasty Omar Pera Background Objetives Features There is a neeed of an account with user/pass for each User user who wants to save his configuration. configuration Storage It is more reasonable for this project to take advantage system of the possibilities of OpenID. Technologies in use Extra possible features
  36. 36. User configuration OpenID MyDasty Omar Pera Background It is a shared identity service Objetives that makes use of a single Features digital identity, eliminating User configuration the need for a different user Storage name and password for each system site. Technologies in use Extra possible features
  37. 37. User configuration OpenID MyDasty Omar Pera Background Objetives The necessity of a database to save different users and Features pass on the system is solved with this service. User configuration The authentication is done by the OpenID provider Storage system of each user. Technologies This way makes our server much secure not storing in use any sensible information. Extra possible features
  38. 38. User configuration OpenID MyDasty Omar Pera Background Objetives The necessity of a database to save different users and Features pass on the system is solved with this service. User configuration The authentication is done by the OpenID provider Storage system of each user. Technologies This way makes our server much secure not storing in use any sensible information. Extra possible features
  39. 39. User configuration OpenID MyDasty Omar Pera Background Objetives The necessity of a database to save different users and Features pass on the system is solved with this service. User configuration The authentication is done by the OpenID provider Storage system of each user. Technologies This way makes our server much secure not storing in use any sensible information. Extra possible features
  40. 40. Storage system MyDasty Omar Pera Background Objetives Features User In order to save the configuration done on MyDasty and configuration comunicate with Dasty2 we need a very simple storage Storage system system. Technologies in use Extra possible features
  41. 41. Storage system MyDasty Omar Pera Background We will give the option to choose about the following Objetives types depending of the use of Dasty2: Features Flat files Ideally for a local copy, just create a User configuration directory and give permission to Apache Storage user to write. system Database Focus on a massive use, a very simple Technologies in use database with one table. Extra possible features Independent of the system storage, we need to set the format of the configuration data: XML, JSON..
  42. 42. Storage system MyDasty Omar Pera Background We will give the option to choose about the following Objetives types depending of the use of Dasty2: Features Flat files Ideally for a local copy, just create a User configuration directory and give permission to Apache Storage user to write. system Database Focus on a massive use, a very simple Technologies in use database with one table. Extra possible features Independent of the system storage, we need to set the format of the configuration data: XML, JSON..
  43. 43. Storage system MyDasty Omar Pera Background We will give the option to choose about the following Objetives types depending of the use of Dasty2: Features Flat files Ideally for a local copy, just create a User configuration directory and give permission to Apache Storage user to write. system Database Focus on a massive use, a very simple Technologies in use database with one table. Extra possible features Independent of the system storage, we need to set the format of the configuration data: XML, JSON..
  44. 44. Storage system MyDasty Omar Pera Background We will give the option to choose about the following Objetives types depending of the use of Dasty2: Features Flat files Ideally for a local copy, just create a User configuration directory and give permission to Apache Storage user to write. system Database Focus on a massive use, a very simple Technologies in use database with one table. Extra possible features Independent of the system storage, we need to set the format of the configuration data: XML, JSON..
  45. 45. Technologies in use MyDasty Omar Pera Background Objetives Server: Features PHP ( optional a database system ) User configuration Client: Storage system XHTML and Cascading Style Sheets (CSS), interaction Technologies in use using the Document Object Model (DOM), AJAX and Extra possible Javascript to bind everything together. features
  46. 46. Extra possible features MyDasty Omar Pera Allow to configure the layout of Dasty2 as well as the default properties. Background Objetives Sort the panels, show or hide panels or columns of the Features graphic, change the width of this columns, etc. User configuration Create an option to configure which DAS reference Storage server to use to retrieve sequence and annotations system (choose between the different Protein coordinates Technologies in use system). Extra possible features Include an option to look for proteins accessions using GO ontologies terms (via OntoDAS software) Display last proteins accession numbers requested on MyDasty for a certain user.
  47. 47. MyDasty Omar Pera Background Objetives Features User configuration Any question, suggestion, idea ? Storage system Technologies in use Extra possible features

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