PRIME Pathway Repository
FAQs

1.  I want to access the repository
2.  I want to convert a pathway into web-publishable format
3.  I want to publish a pathway in the PRIME Pathway Repository
4.  I do not know the image format that BioPP accepts.
5.  I do not know how to export image in CellDesigner 4.0
6.  I do not want to publish my pathway in the PRIME Pathway Repository or store any information regarding the pathway on PRIME Pathway Repository server
7.  I want to update a pathway already existing in the PRIME Pathway Repository
8.  Even after successful conversion of the uploaded pathway, I did not receive the .zip file containing the web-publishable format of the pathway.
9.  I have a Java Virtual Machine (JVM) memory allocation problem.
10.  I have a Mac and I have a Java Virtual Memory (JVM) memory allocation problem.
1.  I want to access the repository
Follow the "Repository" link in the top frame and the link to the desired category
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2.  I want to convert a pathway into web-publishable format
Follow the "Publish" link in the top frame. Note that only registered users can convert a pathway. Follow the link next to the "username" to register.
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3.  I want to publish a pathway in the PRIME Pathway Repository
Choose "Yes" for "Publish on PRIME Pathway Repository" option in the upload form
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4.  I do not know the image format that BioPP accepts.
BioPP tools accept images in .png format only.
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5.  I do not know how to export image in CellDesigner 4.0
The "export image" in CellDesigner 4.0 (alpha) is in the File menu.
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6.  I do not want to publish my pathway in the PRIME Pathway Repository or store any information regarding the pathway on PRIME Pathway Repository server
Choose "No" for "Publish on PRIME Pathway Repository" option in the upload form. Note that neither uploaded information regarding the pathway nor the converted web-publishable format of the pathway is retained on the server after conversion process.
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7.  I want to update a pathway already existing in the PRIME Pathway Repository
An existing pathway can be updated by uploading new pathway files with the existing pathway name and choosing "Yes" for "Have you already published this pathway in our repository" in the upload form. The existing version will be replaced by the currently uploaded version. Note that the original user who created the existing pathway will be permitted to update it.
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8.  Even after successful conversion of the uploaded pathway, I did not receive the .zip file containing the web-publishable format of the pathway.
If "No" was chosen for "Publish on PRIME Pathway Repository" field during the conversion process, the .zip file may be lost due to poor internet connection. Please try converting again to upload the information, the pathway xml file and the pathway image file.

If "Yes" was chosen for "Publish on PRIME Pathway Repository" field during the conversion process, send an email to the administrator with your userID and the name of the pathway requesting the .zip file.
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9.  I have a Java Virtual Machine (JVM) memory allocation problem.
Refer to the help pages in the pathway navigator for help on how to allocate additional memory to the JVM.
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10.  I have a Mac and I have a Java Virtual Memory (JVM) memory allocation problem.
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