|
| 1 | +# Python for Biomolecular Modellers, Parts 1 and 2 |
| 2 | + |
| 3 | +## Aimed at: |
| 4 | +Anyone interested in using Python for Biomodelling. The material in |
| 5 | +this workshop will help you get the most out of the other workshops |
| 6 | +run during the week. |
| 7 | + |
| 8 | +## Requirements: |
| 9 | +Basic knowledge of Python e.g. as in https://chryswoods.com/beginning_python |
| 10 | + |
| 11 | +## Abstract: |
| 12 | +This workshop will introduce more intermediate features of Python that |
| 13 | +are useful for biomolecular modellers. This will include the use of |
| 14 | +Jupyter notebooks, how to write Python functions and classes, and |
| 15 | +how to properly structure, document and test code. The second |
| 16 | +part will introduce you to data analysis tools such as Pandas, |
| 17 | +NumPy and MatplotLib. |
| 18 | + |
| 19 | +## Training Material |
| 20 | + |
| 21 | +The workshop consists of a series of Jupyter notebooks. These are available |
| 22 | +below, and can be run using the |
| 23 | +[workshop jupyter server](https://workshop.biosimspace.org/hub/tmplogin). |
| 24 | + |
| 25 | +Start the server by [clicking here](https://workshop.biosimspace.org/hub/tmplogin). |
| 26 | +This will open a Jupyter notebook interface. Be patient as this may take 30-60 seconds. |
| 27 | +Once this has opened, navigate to the `python_and_data` directory and you will find the |
| 28 | +notebooks there. |
| 29 | + |
| 30 | +The workshops are numbered sequentially from `01_jupyter_howto.ipynb` to |
| 31 | +`17_regular_expressions.ipynb`. They cover a variety of useful Python topics, |
| 32 | +and are *mostly* independent. Feel free to go through them in the order you |
| 33 | +prefer, and to skip topics that you feel you are already comfortable with. |
| 34 | + |
| 35 | +There are exercises in many of the topics. You can find answers in the |
| 36 | +equivalent notebook in the `answers` directory. |
| 37 | + |
| 38 | +Below is a summary of each topic, together with links to view html versions |
| 39 | +of the notebooks the their answers, and to download the notebooks. |
| 40 | + |
| 41 | +While this workshop is running using cloud servers generously supplied |
| 42 | +by [Microsoft Azure](https://azure.microsoft.com/en-us/services/container-service/kubernetes/), |
| 43 | +you can also download and run this workshop on your own computer if |
| 44 | +you are using docker (and your computer has an X86-64 processor that |
| 45 | +supports AVX, e.g. like most Intel processors since 2011). To run on |
| 46 | +your own computer type; |
| 47 | + |
| 48 | +``` |
| 49 | +docker run -it --rm -p 8888:8888 chryswoods/bss-workshop:latest |
| 50 | +``` |
| 51 | + |
| 52 | +This will download the image (may take a while...) and will run it on |
| 53 | +your computer. It will print out the URL of the notebook which you should navigate |
| 54 | +to in your browser (it will look something like `http://localhost:8888/?token=7f4b6be12ff1cec13903d0f27bab2ad7ea3eeaa9f0098dee`) |
| 55 | + |
| 56 | +### [01_jupyter.ipynb](01_jupyter.ipynb) ([answers](answers/01_jupyter.ipynb)) |
| 57 | + |
| 58 | +Introduction to Jupyter notebooks, including how to use the interface, |
| 59 | +how to view molecules, draw graphs, download files, and start a bash |
| 60 | +terminal. |
| 61 | + |
| 62 | +[html](html/01_jupyter.html) | [answers](html/answers/01_jupyter.ipynb) |
| 63 | + |
| 64 | +### [01_jupyter.ipynb](01_jupyter.ipynb) ([answers](answers/01_jupyter.ipynb)) |
| 65 | + |
| 66 | +Introduction to Jupyter notebooks, including how to use the interface, |
| 67 | +how to view molecules, draw graphs, download files, and start a bash |
| 68 | +terminal. |
| 69 | + |
| 70 | +[html](html/01_jupyter.html) | [answers](html/answers/01_jupyter.ipynb) |
| 71 | + |
0 commit comments