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  • Eamonn Maguire 10:13 am on September 27, 2012 Permalink | Reply
    Tags: , , , ISAcreator, metabolights, metabolomics   

    New paper! MetaboLights: towards a new COSMOS of metabolomics data management 

    A new paper, featuring the ISA team as authors is now available to read on MetaboLights (EMBL-EBI metabolomics repository).

    MetaboLights, part of the ISA commons is the new European repository for metabolomic data held at the EBI. Their infrastructure is built upon the ISA software stack, utilising ISAcreator for data entry, ISA-Tab as the format then the BII data manager and database for persistence and storage respectively.

    Click here to access the MetaboLights repository.

     
  • Eamonn Maguire 4:53 pm on September 15, 2011 Permalink | Reply
    Tags: ISAcreator, , Plugins   

    Wooo! ISAcreator is now OSGi enabled for some plugin action! I’ll be writing tutorials on how to create your own plugins in due course! But this is very exciting since I’ve been intending to create a plugin architecture for some time!

     
  • Eamonn Maguire 9:38 am on September 15, 2011 Permalink | Reply
    Tags: Beta testing, ISAcreator,   

    ISAcreator 1.5 beta 2 released for testing 

    Download it:

    Mac https://github.com/downloads/ISA-tools/ISAcreator/ISAcreator-1.5.0.beta2.dmg
    Windows: https://github.com/downloads/ISA-tools/ISAcreator/ISAcreator-1.5.0.beta2-all.zip
    Linux: https://github.com/downloads/ISA-tools/ISAcreator/ISAcreator-1.5.0.beta2-all.zip

    Contains a number of fixes to bugs introduced in beta 1 as a result of new features like autocomplete etc. in the spreadsheet. In 1.5 beta 1, there was a display problem with the file chooser, and the date widget wasn’t inserting dates correctly into the spreadsheet. This has been addressed.

    Moreover, as a result of our desire to integrate conversion and validation components of the infrastructure directly within to ISAcreator has been completed. You can now convert and validate ISAtab files directly from ISAcreator by accessing them in the file menu.

     
  • Eamonn Maguire 5:22 pm on August 18, 2011 Permalink | Reply
    Tags: Autocomplete, , ISAcreator, , , Swing   

    ISAcreator 1.5 in beta testing phase 

    So here’s what’s been added:
    1) ISAvalidator integrated (hence larger file size ~34mb). Access it from the utilities menu item;

    ISAcreator is calling the ISAvalidator component directly now as well as using the standard validation within ISAcreator itself.

    2) New add assay functionality;

    The old subform has been replaced with a new view of the Assays.

    When you click on Create assay, you are now presented with a new component to help you select which assay(s) you wish to add.

    3) New integration with the study sample sheet to look up sample names in autocomplete mode (featuring a new component to build on top of the Java Swing infrastructure to provide better, more customisable autocomplete). Also, if you have factors in your study sample spreadsheet, attached to the sample, these will be propagated automatically to the assay spreadsheet;

    Autocomplete on study samples.

    4) Same autocomplete component is used in protocol ref columns now to look up the protocol name without the clunky widget that was there before.

    Autocomplete on Protocols.

    If you want to test it (please let us know if you have any problems by reporting them in our issue tracker, please download it here!

     
  • Eamonn Maguire 10:24 am on May 13, 2011 Permalink | Reply
    Tags: configurable, , ISAcreator, , JList   

    Configurable form views & reorderable JList 

    Form views are now configurable. In itself, this was quite a bit of work to automatically generate an interface from an XML description. So now, the view like that shown in figure 1 below can be customised like the rest of the ISAcreator views (spreadsheets).

    Figure 1 - ISAcreator form view for entry of Investigation information

    However, after working on this new feature, I realised that due to there being clearly defined sections for Investigation Contacts, Publications etc (see figure 2), it’d be useful if users could move these sections around without having to click forever on a move up button in the ISAconfigurator.

    Figure 2 - configure the form view in the ISAconfigurator

    So, after looking at the Swing Hacks book, which demonstrates how to move single items in a JList, I modified this code and made it possible to move entire blocks up/down in a JList as shown in figure 3 below.

    Figure 3 - Moving an entire section around in the JList

    From what I know, this is the first (at least public) implementation of such a JList. The code can be found on the ISAconfigurator GitHub repository. I will probably move this to its own repository in the next few days when I get a little time.

    Thanks to Joshua Marinacci for allowing me to reuse his code. Check out his new project called Amino, it’s very cool for developing Swing applications. You can even skin UI components using CSS.

     
  • Eamonn Maguire 11:45 am on March 9, 2011 Permalink | Reply
    Tags: ISAcreator, QRcodes   

    ISAcreator can now produce QR codes directly from… 

    ISAcreator can now produce QR codes directly from the tool. For those of you who don’t know what they are, check out the wikipedia entry for QR codes 🙂 We make use of Google’s zxing library.

    You can access the QR codes from the ‘utilities’ item in the menu bar.

    Build up your QR codes contents however you want using the QRcode builder functionality

     
  • Eamonn Maguire 11:38 am on March 9, 2011 Permalink | Reply
    Tags: , , ISAcreator, ISAcreator Configurator, ISAvalidator,   

    New versions of ISAtools released! 

    Access them here 🙂

     
  • Eamonn Maguire 11:03 am on January 5, 2011 Permalink | Reply
    Tags: ISAcreator, JNLP, , webstart   

    Creating an ISAcreator WebStart application 

    One of the advantages of creating a webstart application is that it’s pretty much point and click. From a browser page, users can gain access to your Java tool relatively quickly.

    To deploy a JNLP version of ISAcreator within your organisation, you should follow the following steps…

    1. Get the ISAcreator Jar file you wish to expose via the web.
    2. You need to digitally sign the Jar file using a jarsigner. there are two steps to this process:
    a. Create your key store with an alias (name) using keytool
    keytool -genkey -keystore isatools-keys -alias ISAcreator
    b. Sign the ISAcreator jar file using the key you have just generated
    jarsigner -keystore isatools-keys ISAcreator-1.3.1.jar ISAcreator

    3. Create a JNLP file describing the tool and where the Jar file is located, replacing the baseurl text with the URL of where the ISAcreator.jnlp file etc. are located :

    1. <?xml version="1.0" encoding="utf-8"?> 

    2. <jnlp spec="1.0+" codebase="baseURL" href="ISAcreator.jnlp">

    3. 	<information>

    4. 		<title>ISAcreator 1.3</title>

    5. 		<vendor>ISAtools team, University of Oxford, UK</vendor>

    6. 		<homepage href="http://isatools.org" />

    7. 		<description>ISAcreator</description>

    8. 		<version>1.3</version>

    9. 		<icon href="baseURL/isacreator_logo.jpg"/>

    10. 		<offline-allowed/>

    11. 	</information>

    12. 	<security>

    13. 		<all-permissions/>

    14. 	</security>

    15. 	<resources>

    16. 		<j2se version="1.5+" />

    17. 		<jar href="baseURL/ISAcreator-1.3.1.jar" />

    18. 	</resources>

    19. </jnlp>

    20. 
      

    Now deploy the files to your web server of choice and link to the JNLP file to allow users to download ISAcreator to their machine. An example instance is running at: http://www.antarctic-design.co.uk/isacreator/ISAcreator.jnlp

     
  • Eamonn Maguire 2:43 pm on December 20, 2010 Permalink | Reply
    Tags: , ISAcreator,   

    ISAcreator version 1.3 and ISAconfigurator 1.1 are now available for download! New configurations are also being prepared and will be released shortly to enable easy conformation to MIENS/MIMS/MIGS checklists…more checklists are being created and will be uploaded to a new configuration portal soon!

     
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