Frequently Asked Questions

If you've got questions, we've got answers!

Installation Issues

Genome Compiler requires Adobe AIR, get it here.

Genome Compiler currently supports the following Operating Systems:

  • OSx
  • Windows

Important note for Mountain Lion users: Gatekeeper will report that the application is damaged and will prevent Genome Compiler from running You have to go to System Preferences > Security and Privacy > General. Check “Allow software downloaded from anywhere” to allow Genome Compiler to run. Or use a command line function to change the quarantine attributes. In case you are having problems installing Genome Compiler via the web browser, you can request a download from here Genome Compiler requires Adobe AIR, get it here Please provide a description of what went wrong using our feedback form.

There is a new known issue when trying to install Air files from Chrome – this has been a known issue since the beginning of August 2012.  The issue is related to Google-Adobe collaboration. Download Genome Compiler directly HERE Relevant links: Adobe filed bug – 3310921: https://bugbase.adobe.com/index.cfm?event=bug&id=3310921 Adobe Support Forum: http://forums.adobe.com/message/4618246 Google bug link: http://code.google.com/p/chromium/issues/detail?id=140854&q=air&colspec=ID%20Pri%20Mstone%20ReleaseBlock%20OS%20Area%20Feature%20Status%20Owner%20Summary  

If you try to download Genome Compiler and see the following notification: “Sorry, an error has occurred. The application could not be installed because the installer file is damaged. Try obtaining a new installer file from the application author.” it could be caused by McAffee anti-virus. Disable the firewall and scanning tools and then try again.

Gatekeeper will report that the application is damaged and will prevent Genome Compiler from running You have to go to System Preferences > Security and Privacy > General Check “Allow software downloaded from anywhere” to allow Genome Compiler to run Or use a command line function to change the quarantine attributes.

Import/Export of Genetic Information

Just search: FAQ 1. And press the green arrow to download the record directly into Genome Compiler: FAQ 2 You can also import an NCBI file into Genome Compiler using the “Import” icon. FAQ 3 Genome Compiler currently supports the NCBI INSDSeqXML format.  To get the right file format, go to an NCBI record and perform the following steps: 1) Make sure that on the “Customize View” panel, you have “Show Sequence” ON, and press “Update View” FAQ4 2) Go to Send, complete record, file, INSDSeqXML and press “Create File” FAQ 5 3) Load the file into Genoem Compiler by pressing the “Import” button and selecting the file, or just drag the file (GCproj or INDSxmlSeq) into the material box. FAQ 6 We will also support text, FASTA, and genbank formats in the future release (users can already copy DNA and paste it into a part in the DNA Zoom level).

Just copy a string of DNA letters with no spaces between them from any text editor program, go to Genome Compiler project, create a new part or zoom into the DNA layer of an existing part, and paste the sequence (using the keyboard shortcut or the paste icon) .

Genome Compiler currently supports our own file format (GCproj – default) and plain text file. In order to export a project as a text file, just press the “Export” icon and change the file extension from GCproj to txt. FAQ 7

Miscellaneous

We recommend a minimum resolution of 1366 x 768. At lower resolutions, you can fold in the material box to give yourself a larger workspace.

Genome Compiler uses the following 3rd party libraries:

  • Chris Callendar – Flex 4 Spark Resizable Controls
  • Maxim Kachurovskiy – SparkTree [MIT license]

Nope! Everything you do is your own. The only time we can see what you’ve done is when you send a pricing request, and that’s only so we can quote you a price.

Release 0.3.21

  • Features
    • Track Changes
    • User Comments
    • Display sequence directionality in all zoom levels

Release 0.3.20

Hot fix for 0.3.19

Release 0.3.19

  • Features
    • Edit gene multiple annotations
    • Amino acid & peptide property data to make informed point mutations
    • Bug fixes
      • Various UI fixes
      • Better scrolling
      • Fix clipboard issues

Release 0.3.18

Hot fix for 0.3.17

Release 0.3.17

  • Bug fixes
    • Various crash fixes
    • Better handling of empty parts
    • Fix part split issues
    • Search on minus strand

 

Release 0.3.15

  • Features
    • Combinatorial

Release 0.3.13

  • Features
    • Gene multiple annotations support
    • Amino Acid back translation and codon bias optimization
  • Enhancements
    • Enable editing in Protein View
    • Support more feature keys (PolyA, TATA etc.)

Release 0.3.12

Hotfix for 0.3.11

[plus 0.3.11 release notes]

Release 0.3.11

  • Enhancements
    • Add Tutorials
    • Sharing usability enhancements
  • Bug Fixes
    • Tooltip now works on disabled buttons
    • Fix crash of right click in Amino Acid view
    • Fix crash of drop Parts/Project to new empty project
    • Fix crash of pricing a not-loaded Project (loading from Material Box)

 

Release 0.3.9

Hotfix for 0.3.7

[plus 0.3.7 release notes]

Release 0.3.8

[externally same as 0.3.7]

Release 0.3.7

** Special edition for the Kickstarter Project – Glowing Plant design inside! **

  • Features
    • Primers design
    • Circular view for Plasmids
  • Enhancements
    • Enhance Usability:
      • ‘GoTo’ for better orientation
      • Context menu (Right click)
  • Simpler and faster Pricing flow

Release 0.3.4

  • Enhancements
    • Search in project – support wild cards (n/w/y/etc)
    • NCBI – Support more files
  • Bug fixes
    • Fix error during save
    • Fix error caret issues in DNA view
    • Fix error when moving from Genome to DNA view

Release 0.3.3

[externally same as 0.3.1]

Release 0.3.2

[externally same as 0.3.1]

Release 0.3.1

  • Features
    • Cloud storage and sharing projects capabilities
    • Import whole folders
    • Caret for better editing options in DNA view
  • Enhancements
    • Improve Memory and CPU consumption of the Application
    • Enhance UI:
      • Progress bar for long operations
      • Double click for zoom in
      • Mark Stop Codons in Protein view
  • Enhance search in GeneBank database
  • Bug fixes
    • Fix error after closing non-focused project
    • Fix error after internet connection problem
    • Fix error after project tooltip is shown
    • Fix warning of CDS not divided by 3
    • Fix support of very large bricks

Release 0.2.27

  • Features
    • Cloud storage and sharing projects capabilities
    • Import whole folders
  • Enhancements
    • Improve Memory consumption of the Application
    • Enhance UI – more Tooltips
  • Bug fixes
    • Fix error after selection in Merge brick operation
    • Fix selection after Move Part
    • Fix Error of Undo after Split

Release 0.2.23

  • Features
    • Support for additional file formats – fasta, text, genbank
    • UNDO / REDO for all edit operations
    • Mini-Map for great orientation in Project
    • First time tutorial
  • Enhancements
    • Enrich Inbox files with more parts
    • Enhance Tabs arranging behavior
    • Improve Login flow and Auto-Login mechanism
  • Bug fixes
    • Fix scroll with mouse wheel
    • Drag & Drop between projects

Release 0.2.18

  • Features
    • User folders management in the Material box
    • New visual Project layout – Introducing
      • New tabs concept
      • New  look &  feel for Project properties
      • New abstraction levels approach (Zoom bar)
  • Enhancements
    • Library parts enrichment.
    • Navigation within a project (Arrow keys for all zoom levels)
    • NCBI GenBank Database – improve experience
    • Reduce memory usage
  • Bug fixes
    • Fix upgrade of small files
    • Fix Parsing .gb file
    • Fix rename file error

Release 0.2.16

  • Features
    • User folders management in the Material box
    • New visual Project layout – Introducing
      • New tabs concept
      • New  look &  feel for Project properties
      • New abstraction levels approach (Zoom bar)
  • Enhancements
    • Library parts enrichment.
    • Navigation within a project (Arrow keys for all zoom levels)
    • NCBI GenBank Database – improve experience

Release 0.2.10

  • Features
    • NCBI GenBank Database connection – online search
    • Feature Annotation detection and markers (restriction enzymes cut sites)
    • Multiline view of Project
    • Added library parts – Complete iGem repository of standard biological parts
  • Bug fixes
    • Fix error after long connectivity time
    • Fix error of cut / pasting empty content
    • Fix bug of resize window on low resolution screen
    • Support pasting / dragging DNA sequence with ignored characters (space, tab etc.)
    • Improve velocity Performance
    • Fix DNA search for circular organisms

Release 0.2.5

  • Enhancements
    • Support Import GeneBank format files
    • Enhance experience of highlight selection between zoom levels
  • Fixed Issues
    • Issues focus change between opened Projects
    • Change codon in Amino Acid View bug
    • Paste DNA as text into Brick zoom level
    • Extract Brick out of DNA – fix bug when extracting the last DNA of a Project

Release 0.2.3

  • Enhancements
    • Pricing flow – show the estimated price upfront
    • Update Materials Library
    • Mouse usability – Add usage of Ctrl / Command / Shift when dragging Parts or DNA
    • Keyboard usability – Add use of keyboard for standard actions (copy, cut, paste, delete, save)
    • New Strand icon
    • Add “X” button to clear the Search Box in Materials Library
  • Fixed Issues
    • Removed the underscores from the restriction site DNA sequences
    • Delete last Amino Acid in the Project – fix crash
    • Fix issue when adding a new Brick to an empty project and zoom to DNA after selection
    • Close notifications fix
    • Resize windows fix
    • Fix bug typing DNA on new brick which it is last
    • Fix delete imported files in the Materials Library

Release 0.2.1

  • Fixed Issues
    • GCC Server now serializes projects in the right format.

Release 0.2.0 – Alpha

It might be related to a known problem with Adobe AIR on Windows. Sometimes background processes will set Internet Explorer to “Work Offline” mode. Adobe AIR applications, such as Genome Compiler cannot connect to the internet when Internet Explorer is set to “Work Offline” mode. Even if you never use Internet Explorer, this still affects you.

FAQ 1.

Luckily we have a workaround! To solve this issue follow the steps below:

1. Make sure you are connected to the internet by opening up a search page in a browser.

2. Once you are sure that your computer is connected to the internet, open up Internet Explorer.

3. Navigate to the menu and uncheck “Work Offline”. (Press alt to open Menu) File > Work Offline

If you’d like more information about the problem check out this link:

http://www.badrit.com/blog/2011/1/27/adobe-air-cannot-connect-to-internet-with-error-code-2032

How to Ask Questions?

To submit questions please contact us via: http://genomecompiler.com/feedback support@genomcompiler.com @genomecompiler (twitter)

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