Installing Pathvisio APPs

[jamesvow...@gmail.com]

Hi there,

I am using Wikipathways - Pathvisio quite heavily as a part of my PhD. I am trying to create a document/ tutorial on how I have used Pathvisio and to do this I need to show how to use the MAPP and Wikipathways Apps. I cannot access the Apps from the new Pathvisio website atm. Is there a method of accessing the Apps without the website. 

Best

Krutik

[Martina Summer-Kutmon]

Dear Krutik,

At this moment, it is not possible to install the plugins from the repository. We are moving the repository to a new location so it will hopefully online again soon. For now, you can provide the needed jar files and install them locally (Plugins -> Install local plugins). 

For MAPPBuilder you need to download the latest jar from here: https://github.com/PathVisio/mappbuilder/releases.

For the WikiPathways app, you need to download the main jar file (org.pathvisio.wpclient.jar) and the dependencies.zip file from here: https://github.com/PathVisio/WP-plugin/releases. Make sure all jars are in the same directory, then install them locally. 

Let me know if you have any questions or run into any issues.

Best regards,

Tina

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Martina Summer-Kutmon, PhD
email: mku...@gmail.com

[aisy...@gmail.com]

Hi can you explain step by step on how to install pathvisio locally?

Thank you

Aisya

On Monday, 17 February 2020 14:42:08 UTC, Martina Kutmon wrote:

Dear Krutik,

At this moment, it is not possible to install the plugins from the repository. We are moving the repository to a new location so it will hopefully online again soon. For now, you can provide the needed jar files and install them locally (Plugins -> Install local plugins). 

For MAPPBuilder you need to download the latest jar from here: https://github.com/PathVisio/mappbuilder/releases.

For the WikiPathways app, you need to download the main jar file (org.pathvisio.wpclient.jar) and the dependencies.zip file from here: https://github.com/PathVisio/WP-plugin/releases. Make sure all jars are in the same directory, then install them locally. 

Let me know if you have any questions or run into any issues.

Best regards,

Tina

On Mon, Feb 17, 2020 at 3:34 PM K.P...@newcastle.ac.uk <jamesvow...@gmail.com> wrote:

Hi there,

I am using Wikipathways - Pathvisio quite heavily as a part of my PhD. I am trying to create a document/ tutorial on how I have used Pathvisio and to do this I need to show how to use the MAPP and Wikipathways Apps. I cannot access the Apps from the new Pathvisio website atm. Is there a method of accessing the Apps without the website. 

Best

Krutik

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[Alex Pico]

https://pathvisio.github.io/pages/download

• Current version: PathVisio 3.3.0
• Download the file and unzip it.
• On Windows: start PathVisio by double-clicking the pathvisio.bat file
• On MacOSX / Linux: start PathVisio by running pathvisio.sh or double-click the pathvisio.jar file

 - Alex

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[Aisya Gany]

My bat. file doesnt want to open. what do i do?

Thanks

https://pathvisio.github.io/pages/download

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-----------------------------------------------
Martina Summer-Kutmon, PhD
email: mku...@gmail.com

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Best wishes,

Aisya

[Martina Summer-Kutmon]

Can you provide more information about the error you get? Which operating system / Java version do you use?

Best regards,

Tina

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[jamesvow...@gmail.com]

Thanks a lot, Sorry for the late reply but this was very helpful. 

On Monday, 17 February 2020 14:42:08 UTC, Martina Kutmon wrote:

Dear Krutik,

At this moment, it is not possible to install the plugins from the repository. We are moving the repository to a new location so it will hopefully online again soon. For now, you can provide the needed jar files and install them locally (Plugins -> Install local plugins). 

For MAPPBuilder you need to download the latest jar from here: https://github.com/PathVisio/mappbuilder/releases.

For the WikiPathways app, you need to download the main jar file (org.pathvisio.wpclient.jar) and the dependencies.zip file from here: https://github.com/PathVisio/WP-plugin/releases. Make sure all jars are in the same directory, then install them locally. 

Let me know if you have any questions or run into any issues.

Best regards,

Tina

On Mon, Feb 17, 2020 at 3:34 PM K.P...@newcastle.ac.uk <jamesvow...@gmail.com> wrote:

Hi there,

I am using Wikipathways - Pathvisio quite heavily as a part of my PhD. I am trying to create a document/ tutorial on how I have used Pathvisio and to do this I need to show how to use the MAPP and Wikipathways Apps. I cannot access the Apps from the new Pathvisio website atm. Is there a method of accessing the Apps without the website. 

Best

Krutik

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[Meghan Griffin]

Hi Krutik,

I am just starting to become familiar with PathVisio. I am wondering if you know how to use MAPP once the plugin is installed? I know this is a very basic question but I would really appreciate the help! what do I enter into MAPP ?

best, 

Meghan

[Martina Summer-Kutmon]

Dear Meghan,

I am still working on moving some of the plugin documentation over. Sorry about that.

The MAPPBuilder plugin can be used to create annotated data nodes from a list of genes.

So if you have a table with gene names and identifiers, you only need to add the system code column indicating what identifier it is (https://bridgedb.github.io/pages/system-codes.html). 

If you put the following line (tab separated) in the MAPPBuilder plugin, you will create a gene product with the label TP53 and it will be annotated with its Ensembl identifier so data can be visualized on it.

TP53       ENSG00000141510      En

The aim is to speed up pathway creation by creating annotated data nodes from a list.

Hope this helps and clarifies your questions?

Best, Tina

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