PAML Editor alpha release

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Daniel Bryce

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Feb 17, 2022, 2:00:28 PMFeb 17
to bioprotocols
Dear Colleagues,

I’d like to announce the alpha release of the PAML Editor (PAMLED).  We have two ways to use PAMLED: 

1. https://pamled.sift.net (hosted at SIFT, US only)
2) https://github.com/Bioprotocols/pamled (run locally from source)

Disclaimer: The public server https://pamled.sift.net is currently intended to serve as an evaluation version of PAMLED, and users should assume that user data will NOT be preserved in perpetuity (yet, protocols can be downloaded).  PAMLED manages account credentials through Django (using PBKDF2 encryption) and stores protocol-related data in clear text within a publicly-inaccessible database.  The web application also uses cookies to record session ids.

PAMLED is a web application that supports visual scripting of PAML protocols and has the following features:

- Multiple protocol authoring, saving, deleting, renaming, download, and upload.
- Visual scripting: 
- Drag-and-drop or use context menu (right-click) to select or search for primitives and protocols by name.  
- Link steps with connectors between ports for inputs, outputs, and ordering constraints.  
- Add parameter nodes for constants and connect to inputs, or add input and output nodes to declare protocol inputs and outputs.  
- Select parameter, input, and output names, types and values.
- Use workspace to pan, zoom, move nodes, switch between protocols, and browse primitives list.  
- Primitive authoring: Create a new protocol with only inputs and outputs, and then nest inside another main protocol.
- Protocol nesting: Use primitives or other protocols within your protocol.


In addition to these features, it provides important infrastructure for supporting the editor:

- User account management (creation, log in, log out).
- Database storage of protocols.
- Designed with modern web app tools (React, Bootstrap, Django, and REST).

We are interested in community feedback through email, or issues on the git repository (https://github.com/Bioprotocols/pamled).  There are many improvements we’d like to prioritize for a beta release, and want to serve the community best by gathering input.  Some of the possible features could include:

- Notes fields for primitives, protocols, parameters, inputs, outputs, and ordering relations.
- UI improvements: tooltips, element inspector, container visualization/editing
- Sharing: protocol sharing with groups and world
- Versioning: revision management for protocols.
- Protocol ingest support: paper protocols, or electronic lab notebooks

Please try it out and let us know what you think.  Thanks!

Sincerely,

Dan Bryce
SIFT, LLC.

Mike Fero

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Feb 17, 2022, 3:57:17 PMFeb 17
to Daniel Bryce, bioprotocols
Hi Dan,

This is great! We will take a look.

Mike



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