cadnano's blog

cadnano version 2.2.0

cadnano — Thu, 01 Mar 2012 23:48:43 +0000

The 2.2.0 release of cadnano introduces a new plugin framework to facilitate sharing of user-created extensions of the software. We've included one example plugin to serve as a reference for developing additional plugins, and plan to document everything in a future release. Overall stability of the application is also improved.

Download links

cadnano 2.2.0 installer (OSX)
cadnano 2.2.2 Installer (Windows 32 bit)
cadnano 2.2.0 Installer (Windows 64 bit)
Platform-specific installation instructions are linked from the download page.

AutoBreak Plugin

As a first example plugin, we have written an automatic staple-breaking plugin that introduces breakpoints into the staple strands according to user-specified parameters.
The plugin requires networkx to run. Note to developers: networkx is included in our binaries, but is not included in the git source. You'll need to navigate to the cadnano2/include folder and run "python getdependencies.py" to download the source.

Before AutoBreak:

After AutoBreak:

Developing custom plugins

Please write to us with questions, as this feature is still in the early stages of development and we are happy to help anyone who wants to develop a plugin. We can even help you create a dialog if you're not familiar with Qt.
The best way to start writing a custom plugin is to clone the cadnano2 git repository and get that running on your machine. Next, create a new sub-folder in the plugins directory that follows the same format as the AutoBreak plugin
The plugin adds itself to the menu in __init__.py, and connects its QAction signal to the desired slot. The slot (i.e. the actual plugin code that manipulates the model) can live in a separate file, (see autobreak.py)
Qt Designer can be used to create a custom dialog that accepts input parameters for the plugin. PyQt's pyuic4 can then be used to compile the ui file into python (see our Makefile).

Bug fixes & Updates

Fixed merging of strands that contained loops.
Fixed some subtle bugs with AutoStaple that would crop up later when editing strands downstream.
Patched Windows installer so it can now find Maya and cadnano files not on the C:\.
Fixed bug in which cadnano was using the wrong environment variable to find the home folder in Windows.
Visibility / z-stacking issues with pencil tool.
Applied sequences don't get cleared when breaking or merging strands.
Mousing over a strand now displays its length in the status bar.
Fixed display of insertion sequences in the path view.

Update: 2.1.1

cadnano — Wed, 11 Jan 2012 19:58:05 +0000

We've released a minor update to cadnano to fix a bug where unpaired staple sequences were not exporting as '?' characters.

Download links

cadnano version 2.1

cadnano — Tue, 03 Jan 2012 21:14:33 +0000

After stabilizing the data model in the 2.0 release, we've been busy with some major updates to the cadnano user interface in the last couple months. Read below for what's new.

Download links

Edit: update to 2.1.1

cadnano 2.1.1 installer (OSX)
cadnano 2.1.1 Installer (Windows 32 bit)
cadnano 2.1.1 Installer (Windows 64 bit)
Platform-specific installation instructions are linked from the download page.

New selection-based workflow

The interface for editing strands has been significantly changed. Instead of dragging one endpoint at a time, Strand elements can now be selected and dragged simultaneously.
To extend strands: click and drag to create a rubber-band selection box around the target endpoints, and then click and drag those endpoints as a group.
To resize the entire interface of a structure, select and drag the crossovers. They will snap to "legal" positions.
More explanation and links to example YouTube videos can be found in the docs page.

Selection filters

In order to allow precise selections, we also have added selection filters. You can control whether scaffold and/or staple are selected as well as the the feature type, endpoints, xovers, strands, or helices.

Updated paint tool

Click and drag to paint multiple strands simultaneously.

No more erase tool

Selected objects are removed by pressing the delete key. If a crossover is selected, it will be removed but leave strands intact. If one or both endpoints of a strand is selected, the entire strand will be deleted.

Status bar

Mouse over a position to display the coordinate.
The "delta" is displayed when dragging selected items.

Automatic scaffold creation

Cadnano will attempt to "pre-populate" some scaffold strands when you click and drag in the lattice panel.
Rasterization style can be chosen in the Preferences.
Use undo to revert to the 3-base stubs.

Appearance changes

Path endpoints drawn with a border to make them easier to see when zoomed out.
Sequence labels have been moved "inside" the strand grid in the path view.
Vertical grid lines are drawn thicker near default staple crossovers (every 7 bases for honeycomb lattice and 8 bases for square lattice).
Zoom level of detail: grid lines are hidden when zoomed out to make features easier to distinguish.
Removed some extra file menus & items.
Added "about cadnano" dialog.

Performance improvements

Autostaple is faster. It had slowed down significantly compared to cadnano1 due to the new data model architecture. It's still not as fast as the original, but future optimizations should be possible.
Moving items is faster after disabling QGraphicsScene Item Indexing

Bug fixes

Fixed a bug in osx installer causing re-installs to fail.
Fixed bug causing crash when creating new document in maya
Fixed bug causing some icons to not display.
Fixed bug causing paint tool to switch to black if color dialog was canceled.
Fixed bug causing parts to resize smaller improperly.
Fixed bug with strand merging.