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.

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. 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. 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. 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. 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. 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. 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. 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. 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. MyDasty
Omar Pera
Background
Objetives
Features
User
How to improve this search page?
configuration
Storage
MyDasty
system
Technologies
in use
Extra possible
features

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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. MyDasty
Omar Pera
Background
Objetives
Features
User
configuration
Any question, suggestion, idea ?
Storage
system
Technologies
in use
Extra possible
features