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ChemGPS-NP Web is a system for computing the eight principal components (dimensions) describing physical-chemical properties for a reference set of compounds. The technical details is described on page 7-9 in the EMBnet.news article from 2008.

ChemGPS-NP EMBnet.news

In this second generation of ChemGPS-NP Web the previous queue service has been complemented with the molecule and convexity service.

Web interface

The web interface provides the job queue as its main component. Jobs are enqueued by submitting molecules in SMILES-format (suffixed with an optional name) one per row. The input data can be posted using the form, by uploading file(s) or submitting download URL's.

For each file or URL submitted, a separate job will be enqueue. Use the queue interface for monitor status or download result. The 3D plot tool (requires WebGL support ) can then be used to visualize the predicted positions from 8D space by selecting three of the available dimensions for projection.

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Convexity

The convexity test is a new feature for checking whether a given set of positions are within one or more reference (convex) set of points. Clicking on the "inside" button in the queue listing opens up this tool. It's also possible to perform this calculation by submitting positions for a convexity task using the standard web interface for submitting jobs.

Web services

The sub system for queue, molecules and convexity is also available as web services. The queue comes with both JSON and SOAP interface, while the latter two is only available as JSON services.

Getting started with these API is simple and can be tested direct from the command line using curl. All three API is fully described with many examples.

API documentation

Usage contract

By using this system you agree with that submitted compounds (molecules in smiles format) is collected and included in the molecules database. These collected compounds might also be used in other circumstances and published later by the system owner.

Sharing queues

Each used can define one or more queues to use as a container for their submitted jobs. A default queue will be used unless a queue is selected. By selecting the same queue name, the queue can be shared between co-workers. Switching queue is done from the web interface by clicking on the "reverse clock" icon in the main menu bar.
Default queue
If no queue is specified, then a default queue based on connecting IP-address is used. Chosing "revert" from web interface or passing null for select method in web service API will reset used queue to default.
Further reading
The select queue page contains further information on queue switching, both from user interface and from web services.

Select queue

Cookies

Cookies are used to identify the current selected queue. The cookie (hostid) is not direclty connected with any sensitive information, but each hostid has on server side a stored mapping to the IP-address. The queue name to hostid (hash) is not stored though.

Tool chain changes

The command pipeline is now using Dragon 7 that calculates slightly different descriptor values used as input for SIMCA-QP. Approximate 97% of predicted positions are within 10% difference though as compared to previous version of ChemGPS-NP Web. A positive effect is that fewer SMILES-strings are now rejected.

Migrate

Queues (containing result and input data) from previous version of ChemGPS-NP Web has not been migrated, but the old version is still accessable for those who wish to recalculate positions using the updated tool chain. Simply copy the indata from your old queues and submit as a new job in this version.

Previous version

Web browsers

Using Mozilla Firefox, Google Chrome, Safari and Microsoft Edge should work. Using Android and Safari (on iOS) might work partially due to limited hardware (WebGL might not be supported).

Internet Explorer will probably never work because of missing support for some web standards (i.e. promises). No plans exists at the moment to add polyfills just to get IE to work. Use an alternative browser instead.