Using the SwissCellPrediction Webserver

1. Checking that the server is up and running

a. The importance of being open to the world

Greetings: Hello World! If the Web server is up and running, you will receive a "Hello World!" message. If not, please contact the SwissCellPrediction team.

b. The importance of good science

George Box said it all: All models are wrong, but some are useful.
George Edward Pelham Box If the Web server is up and running, you will receive a famous quote by George Box as message. If not, please contact the SwissCellPrediction team.

c. The importance of love

Charles Darwin said it all: The love for all living creatures is the most noble attribute of man.
Charles Robert Darwin If the Web server is up and running, you will receive a beautiful quote by Charles Darwin as message. If not, please contact the SwissCellPrediction team.

2. Starting SwissCellPrediction to look for sensitive cell line targets of a query molecule

You can launch the SwissCellPrediction machinery using the startcytox command below:

a. Similarity-based reverse virtual screening for targeted therapy

We will use the Ponatinib molecule, with the following SMILES as an example:

CN1CCN(Cc2ccc(NC(=O)c3ccc(C)c(c3)C#Cc3cnc4cccnn34)cc2C(F)(F)F)CC1 Session number: 42219790
To check your session status, please run the following command:
curl "SwissCellPrediction.ch:1234/checksession?sessionNumber=42219790"
The similarity-based reverse virtual screening has been completed.
where:

• smiles is the SMILES of the small molecule (Ponatinib in our example)

b. Recognition of non-specific anticancer chemical signature for chemotherapy

If your query molecule is recognized as harboring an anticancer chemical signature associated with a non-specific mode of action, SwissCellPrediction provides a list of cell lines which have been experimentally shown to be sensitive against some other compounds harboring the same non-specific anticancer flags as the query molecule.

It is the case for instance for the Doxorubicin molecule, with the following SMILES:

COc1cccc2c1C(=O)c1c(O)c3c(c(O)c1C2=O)C[C@@](O)(C(=O)CO)C[C@@H]3O[C@H]1C[C@H](N)[C@H](O)[C@H](C)O1

Please check question 13 of our FAQ for more details. Session number: 37645967
To check your session status, please run the following command:
curl "SwissCellPrediction.ch:1234/checksession?sessionNumber=37645967" Your compound has been flagged harboring a non-specific anticancer chemical signature.
Please check question 13 of our FAQ for more details: http://SwissCellPrediction.ch/FAQ.php where:

• smiles is the SMILES of the small molecule (Doxorubicin in our example)

3. Checking the status of your SwissCellPrediction job

You can check the status of the job using the Session Number that you have received upon submission. If the calculation is pending in the queue waiting for its turn, you will be informed about that, and you will be provided with the number of jobs that are waiting before it in the queue. If the job is currently running, you will be informed about that and the running time will be reported. If the calculation is over, you will be also informed that the job is finished. Your parameters:
  Query: smiles
  Input: CN1CCN(Cc2ccc(NC(=O)c3ccc(C)c(c3)C#Cc3cnc4cccnn34)cc2C(F)(F)F)CC1
  Date: Mon 18 Mar 2024 10:48:15

Calculation is in the queue. Number of jobs before yours: 12 Your parameters:
  Query: smiles
  Input: CN1CCN(Cc2ccc(NC(=O)c3ccc(C)c(c3)C#Cc3cnc4cccnn34)cc2C(F)(F)F)CC1
  Date: Mon 18 Mar 2024 10:48:15

Calculation currently running. Run time: 0:02 Your parameters:
  Query: smiles
  Input: CN1CCN(Cc2ccc(NC(=O)c3ccc(C)c(c3)C#Cc3cnc4cccnn34)cc2C(F)(F)F)CC1
  Date: Wed 25 Jun 2025 10:20:21

Calculation is finished
To retrieve the results, please run the following command:
curl "SwissCellPrediction.ch:1234/retrievesession?sessionNumber=65720367" -o results.tar.gz

4. Cancelling a SwissCellPrediction job

You can cancel the job that is currently running or pending in the queue. The following command will remove the calculation from the queue of the server: Calculation of session 1742524 was cancelled

5. Retrieving the results of a SwissCellPrediction job

After you have confirmed that your submitted job is finished (see above), you can retrieve the results: Your parameters:
  Query: smiles
  Input: CN1CCN(Cc2ccc(NC(=O)c3ccc(C)c(c3)C#Cc3cnc4cccnn34)cc2C(F)(F)F)CC1
  Date: Wed 25 Jun 2025 10:20:21

Calculation is finished.
To retrieve the results, please run the following command:
curl "SwissCellPrediction.ch:1234/retrievesession?sessionNumber=65720367" -o results.tar.gz Simply run the given command to retrieve your results:
You will download the gzip results file on your machine.