Hi everyone. Hope you are doing well.
I would like to share with you some importante knowledge I have got on bionformatics; the use of Terra platform.
How to use Terra (Terra.Bio)
Terra.Bio is a cloud-based platform for biomedical research that offers a variety of features to support scientific research.
Some of the key features of Terra.Bio:
Collaboration: provides a shared space for researchers to collaborate on projects, with built-in security features to protect sensitive data. Here is a video that summarizes how this can be done.
Access to data: offers access to a wide range of public and access-controlled datasets, including key research datasets in medical and population genetics.
Interactive analysis tools: Jupyter Notebooks, RStudio, and Galaxy, which is a popular open-source bioinformatics applications.
Workflow management: supports the creation and management of workflows, which can help researchers automate complex analyses and ensure reproducibility.
Educational resources: offers a variety of educational resources, including video tutorials, webinars, and online courses, to help researchers get up to speed quickly. You can see in this tutorial how it is done.
To understand a bit more on Terra, you should see it´s architecture that is explained in this video, or you can see in this picture:
Some important practical points when using Terra:
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Terra is the platform between the cloud and the user, so you can access the data in the buckets, that is where the data exists in the cloud.
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Terra has a mix of code and markdown cells you can run
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You cannot download data
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You need to start a VM to copy data over
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You can upload your own data, and that stays in your bucket
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Only other people in your workspaces and billing project can access the data in your bucket
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You pay for analyses
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For analyses that last hours, you want to submit a WDL
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You can program in any of the following languages in a Jupyter notebook (once set up properly)
- Python (will see in analysis modules)
- R (will see in analysis modules)
- bash (will see in analysis modules)
- WDL (will introduce in last module)
- SQL/BigQuery
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You can save your notebook as an .ipynb (native format) or HTML (can open in a browser)
Some downsides that Terra has are:
- Sometimes it works slow or there are shutdowns
- If you are working with other in the same notebook, it gets slower
- You have to pay for the analysis
Hope this topic helps, and if you have any question, please feel free to reach out.