In your research laboratory, time is a precious commodity. Every moment spent on mundane tasks is a moment lost in the pursuit of scientific breakthroughs. But what if I told you there's a tool capable of revolutionizing your workflow? Enter Python scripting within SciSpot's integrated JupyterHub environment.
In this training article, we'll explore how Python scripts breathe new life into lab management. Using your JupyterHub credentials provided securely by Scispot, you can develop Python scripts tailored to your specific lab management needs. Whether it's automating data entry, optimizing inventory, or tracking samples, the possibilities are endless. Join us as we uncover the power of Python in the pursuit of scientific excellence.
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How do I create and execute my scripts?
To begin, navigate to the Jupyter Notebook app within Scispot.
Here, you will be able to create Executables, which you can run within the Scispot platform to automate your workflow, or Scripts, simple Python files for any of your computing needs, which you can publish into Executables if needed.
To create a new script click on the " + Create New" button and select "Script". You will be directed to log in to JupyterHub.
Once you do so, you will see a dashboard of all of your scripts. Here you can create new ones or upload your existing scripts:
Once you've written your script, simply publish it as an executable within the Scispot platform.
This executable can then be run on demand or triggered automatically based on predefined conditions.
How do I run my Executables on demand?
You have two options, either go to the chosen Labsheets directly, click on Jupyter Notebook in the top-right corner and select your script to run:
Or, navigate to the Jupyter Notebook homepage within Scispot and run your scripts from there:
How do I set up triggers?
Navigate to the Automation button in any of your Labsheets and select Triggers for the dropdown.
Here, you can create triggers that initiate the execution of your Python scripts.
Assign a name to your trigger, specify the user(s) who will receive a notification once the script begins and ends execution, and attach the Jupyter script you wish to execute.
You can also define rules for when the trigger should be activated.
Note: We only support triggers in Labsheets, not Labspaces.
Need some rule inspiration?
Inventory Replenishment: Set up a rule to trigger a Python script that analyzes inventory levels and automatically places orders for replenishment when stock falls below a certain threshold.
Sample Temperature Monitoring: Define a rule that triggers a Python script to monitor the temperature of stored samples. If the temperature exceeds predefined limits, notifications are sent to designated users for immediate action.
Experiment Creation: Create a rule to trigger a Python script that creates experiments or protocols based on the availability of equipment and resources. Notifications can be sent to lab personnel to confirm scheduling and allocation.
Quality Control Checks: Implement a rule to trigger a Python script that performs regular quality control checks on lab equipment. If any abnormalities are detected, alerts are sent to maintenance staff for prompt attention.
Data Analysis and Reporting: Define rules to trigger Python scripts for automated data analysis and reporting. Generate custom reports on experimental results, trends, and insights, with notifications sent to relevant stakeholders.
Where can I see my error logs?
Add a print statement to your script to see the logs in our Jupyter Notebook. Simply navigate to the script you just executed, click on the three dots and select "Show Output".
Can I integrate my scripts with Github?
Yes! More details in the article here
For more info, FAQs, and common code snippets, check out our blog here.
Ready to revolutionize your lab workflows? Get started with Scispot and JupyterHub now!
Note: For security purposes, ensure that Jupyter Hub credentials are handled and stored securely according to best practices.
NOTE: Not every account will have these integrations. Please contact [email protected] if you don't see these features enabled.