Cytoscape v3.3 Prerelease Available
Barry Demchak
Hello Cytoscapers –
We’re charging hard towards releasing Cytoscape v3.3 – the target date is around two weeks from now.
Ahead of that, we’ll do more rounds of testing, and we’re hoping that you’ll take a look, too.
For app developers: an early look is especially important so you can tell us if we broke something your app depends on – it’s unlikely, but if it’s true, we’d like to know ASAP.
Please feel free to download and try out v3.3.0-SNAPSHOT at http://tinyurl.com/p3kkmfx. Note that this is a ZIP file, not a complete installer. You will need to UNZIP it to a folder.
Note that v3.3 REQUIRES Java 8. If you’re running on a 64 bit system, you can find it here: http://java.com/en/download/manual.jsp
We look forward to your enjoying this excellent release and giving us the feedback we need.
Here’s a brief summary of the changes in v3.3:
Features
· Several big and small changes to improve network import and filtering
§ Importing networks and tables from a file has a much easier and attractive interface
§ Key columns are now better matched when importing table data
§ Filters now enable selection based on properties of adjacent nodes
§ Filtering can now be done in stages, adding or removing node selections
· Default layout is now Prefuse and views are automatically created for all but the biggest networks
· Many dialog boxes have been improved for aesthetics and consistency
· GPU support for much faster Prefuse layouts (assumes late model GPU and appropriate drivers)
· Several core features are now repackaged as “core apps” and will be available in the App Store. This will allow us to update more parts of Cytoscape more often than the normal release cycle.
· Cytoscape will automatically detect when the App Store has a newer version of an app you have installed, and then let you know
· cyREST is now a “core app”, so you won’t need to install it anymore. The Command scripts execution engine is now a “core app”, too, so it can evolve more quickly than before.
· Cytoscape’s App Manager (i.e., the App menu item) has been substantially changed under the hood, though hopefully so that no one will notice
Over 160 Issues addressed, including:
· Numerous UI consistency & operational issues
· Improvements in Group settings & visualization
· New DOT file reader
· Updated BioGrid files
· New functions: InDegree, OutDegree, SourceID, TargetID
· Marching ant animation for edges
· Removing duplicate edges much faster
· More and better arrows on directed edges
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
: Barry Demchak, PhD
: National Resource for Network Biology (NRNB)
: UC San Diego
: Department of Medicine
: Medical Sciences Research (MSR) Building, Room 3A15
: https://sosa.ucsd.edu/confluence/display/~bdemchak/Home
: Land line: (858) 822-4756, Mobile: (858) 452-8700
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Matthias König
I just downloaded the 3.3 snapshot (cytoscape-3.3.0-20151102.210809-713.tar.gz) and tried on ubuntu 64bit system with AMD-Catalyst-15.9-Linux-installer-15.201.1151-x86.x86_64
1. try fatal error (see log attached)
Tying to import network resulted in
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007f7ab8050af8, pid=30062, tid=140165632669440
#
# JRE version: Java(TM) SE Runtime Environment (8.0_66-b17) (build 1.8.0_66-b17)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.66-b17 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C [libOpenCL.so+0x4af8] clReleaseMemObject+0x8
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home/mkoenig/Programs/cytoscape-unix-3.3.0-SNAPSHOT/hs_err_pid30062.log
#
# If you would like to submit a bug report, please visit:
# http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
./cytoscape.sh: line 80: 30062 Aborted $script_path/framework/bin/karaf "$@"
2. try and 3. try
Cytoscape suddenly crashes with
*** Error in `/usr/bin/java': corrupted double-linked list: 0x00007f9aa4be73f0 ***
./cytoscape.sh: line 80: 30942 Aborted $script_path/framework/bin/karaf "$@"
This snapshot is not working for me. Crashing all the time. Came not even to the point of testing apps.
I just extracted the tar.gz and run ./cytoscape.sh, not sure if I did something wrong here.
The best
Matthias
Barry Demchak
Hi, Matthias –
Thank you *very* much for the feedback. We’ll take a look at this ASAP. We’re having no trouble with this on Windows and Mac platforms. We’re also successful with building and executing on Fedora. We’ll be very interested to see what’s going on here.
(Note that before we release in the next few weeks, we’ll be demonstrating correct operation on 37 different platforms, about 1/3 of which are Linux. So, we have a few checks and balances built into the process. Your early feedback is very helpful.)
Thanks!
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