Announcing Cytoscape 3.6.1 !

[Barry Demchak]

=+=+ =+=+ =+=+ =+=+ = Hello Cytoscapers! =+=+ =+=+ =+=+ =+=+ =+=+

 

We're very pleased and excited to announce availability of Cytoscape v3.6.1, effective immediately!

 

To get a copy, surf to http://cytoscape.org/download.php, and download and execute the installer for your workstation.

 

The main focus of v3.6.1 is to make several key features available ahead of the next full release (v3.7, later this year):

 

·         Automatic Java 8 installation for Windows & Mac

 

·         Native support for loading and saving networks in NDEx

 

·         Fixes for

o    2 finger zoom on Mac

o    Diffusion Heat/Rank modality issues

o    Cytoscape Automation and Commands APIs

 

Note that with v3.6.1, Windows & Mac systems can run Java 9 or 10 without conflicting with Cytoscape -- it installs and uses a private Java 8.

 

For Linux, you must be sure Java 8 is installed and is first on the PATH or is named via the JAVA_HOME environment variable.

 

v3.6.1 still supports 32 bit systems such as Windows XP.

 

If you find any issues with this release, please let us know by posting to cytoscape...@googlegroups.com … we very much value your feedback!

 

Please check the v3.6.1 materials in our Welcome Letter (http://www.cytoscape.org/cy3_welcome_letter_v19.pdf) and the Release Notes (http://www.cytoscape.org/release_notes_3_6_1.html).

 

Tell all your friends ...

 

We appreciate your checking this out, and we hope you find it as great to work with as we do!

 

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: Barry Demchak, PhD

: National Resource for Network Biology (NRNB)

: UC San Diego

: Department of Medicine

: Biomedical Research Facility II, Room 3A15

: http://orcid.org/0000-0001-7065-7786

: Land line: (858) 822-4756, Mobile: (858) 452-8700

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[diyoyo]

Hi, it seems like if you don't set up a JAVA_HOME in advance, the cytoscape.bat tries to edit the registry, in Windows. It is quite problematic when you don't have administrator privileges.

On Wednesday, March 28, 2018 at 1:38:27 AM UTC+2, Barry Demchak wrote:

=+=+ =+=+ =+=+ =+=+ = Hello Cytoscapers! =+=+ =+=+ =+=+ =+=+ =+=+

 

We're very pleased and excited to announce availability of Cytoscape v3.6.1, effective immediately!

 

To get a copy, surf to http://cytoscape.org/download.php, and download and execute the installer for your workstation.

 

The main focus of v3.6.1 is to make several key features available ahead of the next full release (v3.7, later this year):

 

·         Automatic Java 8 installation for Windows & Mac

 

·         Native support for loading and saving networks in NDEx

 

·         Fixes for

o    2 finger zoom on Mac

o    Diffusion Heat/Rank modality issues

o    Cytoscape Automation and Commands APIs

 

Note that with v3.6.1, Windows & Mac systems can run Java 9 or 10 without conflicting with Cytoscape -- it installs and uses a private Java 8.

 

For Linux, you must be sure Java 8 is installed and is first on the PATH or is named via the JAVA_HOME environment variable.

 

v3.6.1 still supports 32 bit systems such as Windows XP.

 

If you find any issues with this release, please let us know by posting to cytoscape-helpdesk@googlegroups.com … we very much value your feedback!

[Barry Demchak]

Hi --

I don't think I'm seeing the same things you are. Could you explain more about why you think the .bat is *editing* the registry???

You're right that if JAVA_HOME isn't set, then the .bat does more work. The first thing it does is look for a private JVM in the /Program Files/Common Files/i4j_res directory. If it finds an appropriate Java8, it uses it.

If not, it looks in the registry to see if there is a "current JVM", and if so, whether it's a Java8 we can use. The registry access is "query", and not one of the other reg calls.

If it's editing the registry, I'd very much like to know more. You're right ... that would be a real problem.

Thanks!

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--

vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
: Barry Demchak, PhD
: National Resource for Network Biology (NRNB)
: UC San Diego
: Department of Medicine
: Biomedical Research Facility II, Room 3A15
: http://orcid.org/0000-0001-7065-7786

: Land line: (858) 822-4756, Mobile: (858) 452-8700

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^