diff --git a/.gitignore b/.gitignore index 4df4b39..5430fb2 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,4 @@ .gitattributes __pycache__ *.swp +*.ziggy diff --git a/modules/module1/InClass/Index.ipynb b/modules/module1/InClass/Index.ipynb index 1726f9d..f3bb4d1 100644 --- a/modules/module1/InClass/Index.ipynb +++ b/modules/module1/InClass/Index.ipynb @@ -54,7 +54,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.2" + "version": "3.7.3" }, "latex_envs": { "LaTeX_envs_menu_present": true, diff --git a/modules/module1/InClass/environment_variables.ipynb b/modules/module1/InClass/environment_variables.ipynb index 65b68be..839cd13 100644 --- a/modules/module1/InClass/environment_variables.ipynb +++ b/modules/module1/InClass/environment_variables.ipynb @@ -31,6 +31,7 @@ "outputs": [], "source": [ "%%bash\n", + "\n", "echo $HOME\n", "echo $PATH" ] @@ -239,10 +240,10 @@ "outputs": [], "source": [ "%%bash\n", - "rm -r /home/jovyan/bin\n", - "mkdir /home/jovyan/bin\n", - "cp ./ls /home/jovyan/bin/.\n", - "chmod +x /home/jovyan/bin/ls" + "rm -r /home/mdsung/bin\n", + "mkdir /home/mdsung/bin\n", + "cp ./ls /home/mdsung/bin/.\n", + "chmod +x /home/mdsung/bin/ls" ] }, { @@ -252,7 +253,8 @@ "outputs": [], "source": [ "%%bash\n", - "/home/jovyan/bin/ls" + "pwd\n", + "/home/mdsung/bin/ls" ] }, { @@ -295,7 +297,7 @@ "echo $PATH\n", "export PATH=$PATH:/home/jovyan/bin\n", "which ls\n", - "ls /home/jovyan/DATA/Misc\n" + "ls /home/mdsung/DATA/Misc\n" ] }, { @@ -325,7 +327,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module1/InClass/finding_files.ipynb b/modules/module1/InClass/finding_files.ipynb index 6de8ea5..bc9936c 100644 --- a/modules/module1/InClass/finding_files.ipynb +++ b/modules/module1/InClass/finding_files.ipynb @@ -81,17 +81,6 @@ "If I do not provide any expressions, all files under the specified print will be found." ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "%%bash\n", - "\n", - "find . " - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -128,7 +117,7 @@ "outputs": [], "source": [ "%%bash\n", - "find /home/jovyan -name 'README'" + "find /home/mdsung -name 'README'" ] }, { @@ -172,7 +161,7 @@ "outputs": [], "source": [ "%%bash\n", - "find /home/jovyan/work/decart_bootcamp_part1 -name '*.ipynb'\n" + "find /home/mdsung/2019_linux_bootcamp -name '*.ipynb'\n" ] }, { @@ -190,7 +179,7 @@ "source": [ "## Exercise\n", "\n", - "In the /home/jovyan/DATA directory there are [WAVE files](https://en.wikipedia.org/wiki/WAV) (.wav) that are recordings of various heart anomalies. There are two types of Mitral valve problems: mitral stenosis (ms) and mitral regurgitation (mr). Use find with wildcards to find all the \"ms\" and \"mr\" WAVE files. Make sure that you do not match other files, for example pulmonary stenosis (ps). How many mitral WAVE files are there? How many WAVE files are there?" + "In the /home/mdsung/DATA directory there are [WAVE files](https://en.wikipedia.org/wiki/WAV) (.wav) that are recordings of various heart anomalies. There are two types of Mitral valve problems: mitral stenosis (ms) and mitral regurgitation (mr). Use find with wildcards to find all the \"ms\" and \"mr\" WAVE files. Make sure that you do not match other files, for example pulmonary stenosis (ps). How many mitral WAVE files are there? How many WAVE files are there?" ] }, { @@ -199,7 +188,8 @@ "metadata": {}, "outputs": [], "source": [ - "%%bash\n" + "%%bash\n", + "find /home/mdsung/DATA -name '*ms*.*'" ] }, { @@ -208,7 +198,8 @@ "metadata": {}, "outputs": [], "source": [ - "mitral_files()" + "%%bash\n", + "find /home/mdsung/DATA -name '*mr*.*'" ] }, { @@ -217,7 +208,16 @@ "metadata": {}, "outputs": [], "source": [ - "wave_files()" + "mitral_files(2)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "wave_files(11)" ] }, { @@ -258,7 +258,8 @@ "metadata": {}, "outputs": [], "source": [ - "%%bash" + "%%bash\n", + "find ~/DATA -size 10000 -name '*.txt'" ] }, { @@ -267,7 +268,7 @@ "metadata": {}, "outputs": [], "source": [ - "find_10k_files()" + "find_10k_files(66)" ] }, { @@ -317,7 +318,7 @@ "outputs": [], "source": [ "%%bash\n", - "grep chapel /home/jovyan/DATA/Misc/obits.txt" + "grep chapel /home/mdsung/DATA/Misc/obits.txt" ] }, { @@ -334,7 +335,7 @@ "outputs": [], "source": [ "%%bash\n", - "grep -i chapel /home/jovyan/DATA/Misc/obits.txt" + "grep -i chapel /home/mdsung/DATA/Misc/obits.txt" ] }, { @@ -351,7 +352,7 @@ "outputs": [], "source": [ "%%bash\n", - "grep -i -c chapel /home/jovyan/DATA/Misc/obits.txt" + "grep -i -c chapel /home/mdsung/DATA/Misc/obits.txt" ] }, { @@ -368,7 +369,7 @@ "outputs": [], "source": [ "%%bash\n", - "grep -i -c -r chapel /home/jovyan/DATA/Misc" + "grep -i -c -r chapel /home/mdsung/DATA/Misc" ] }, { @@ -385,7 +386,7 @@ "outputs": [], "source": [ "%%bash\n", - "grep -i -l -r chapel /home/jovyan/DATA/Misc" + "grep -i -l -r chapel /home/mdsung/DATA/Misc" ] }, { @@ -402,8 +403,8 @@ "outputs": [], "source": [ "%%bash\n", - "grep -i chapel /home/jovyan/DATA/Misc/obits.txt \\\n", - "/home/jovyan/DATA/Misc/icd9-short.txt" + "grep -i chapel /home/mdsung/DATA/Misc/obits.txt \\\n", + "/home/mdsung/DATA/Misc/icd9-short.txt" ] }, { @@ -413,7 +414,7 @@ "outputs": [], "source": [ "%%bash\n", - "grep -i chapel /home/jovyan/DATA/Misc/*.txt" + "grep -i chapel /home/mdsung/DATA/Misc/*.txt" ] }, { @@ -434,7 +435,7 @@ "outputs": [], "source": [ "%%bash\n", - "grep '7.-year-old' /home/jovyan/DATA/Misc/*.txt" + "grep '7.-year-old' /home/mdsung/DATA/Misc/*.txt" ] }, { @@ -458,7 +459,11 @@ "metadata": {}, "outputs": [], "source": [ - "bp_hr_ge200()" + "cd /home/mdsung/DATA/Numerics/mimic2/hr/subjects\n", + "grep -lrP \"\\b(? ~/hr200.txt ##\\b : word boundary \n", + "cd /home/mdsung/DATA/Numerics/mimic2/bp/subjects\n", + "grep -lrP \"\\b(? ~/bp200.txt\n", + "grep -Fx -f ~/bp200.txt ~/hr200.txt" ] }, { @@ -466,7 +471,9 @@ "execution_count": null, "metadata": {}, "outputs": [], - "source": [] + "source": [ + "bp_hr_ge200()" + ] } ], "metadata": { @@ -485,7 +492,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.5" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module1/InClass/introducing_shells.ipynb b/modules/module1/InClass/introducing_shells.ipynb index 13f3fa7..f2f0d09 100644 --- a/modules/module1/InClass/introducing_shells.ipynb +++ b/modules/module1/InClass/introducing_shells.ipynb @@ -86,7 +86,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.2" + "version": "3.7.3" }, "latex_envs": { "LaTeX_envs_menu_present": true, diff --git a/modules/module1/InClass/navigating_file_system.ipynb b/modules/module1/InClass/navigating_file_system.ipynb index a15b9db..08076b3 100644 --- a/modules/module1/InClass/navigating_file_system.ipynb +++ b/modules/module1/InClass/navigating_file_system.ipynb @@ -287,9 +287,9 @@ "metadata": {}, "outputs": [], "source": [ - "number_of_files = -1\n", - "largest_file = \"None\"\n", - "most_recent_file = \"None\"" + "number_of_files = 8\n", + "largest_file = \"Accidents7904.csv\"\n", + "most_recent_file = \"seinfeldFood.sqlite\"" ] }, { @@ -469,7 +469,8 @@ "outputs": [], "source": [ "%%bash\n", - "ls -ltr /home/jovyan/DATA/Misc" + "mkdir -p ./OutbreakDetection/{Chiefcomplaints,Obituaries,Sales,SocialMedia/Twitter}\n", + "tree" ] }, { @@ -643,6 +644,17 @@ "```" ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "cd ~/work/OutbreakDetection\n", + "echo -e \"# Outbreak Detector\\nThis directory contains data for developing an outbreak detector.\" > README.md" + ] + }, { "cell_type": "code", "execution_count": null, @@ -700,6 +712,16 @@ "Use `mv` to rename the `Sales` to `DrugSales`." ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "mv Sales DrugSales" + ] + }, { "cell_type": "code", "execution_count": null, @@ -737,6 +759,16 @@ "Make a backup of the ``OutbreakDetection`` in your home directory named ``OutbreakDetectionBackup``." ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "cp -r ~/work/OutbreakDetection/ ~/OutbreakDetectionBackup" + ] + }, { "cell_type": "code", "execution_count": null, @@ -752,7 +784,7 @@ "source": [ "## Exercise\n", "\n", - "In ``/home/jovyan/DATA/Misc`` there is a file name ``obits.txt``. Use the ``mv`` command to move the ``obits.txt`` file to the ``OutbreakDetection/Obituaries`` directory." + "In ``/home/mindong/DATA/Misc`` there is a file name ``obits.txt``. Use the ``mv`` command to move the ``obits.txt`` file to the ``OutbreakDetection/Obituaries`` directory." ] }, { @@ -762,7 +794,8 @@ "outputs": [], "source": [ "%%bash\n", - "# Write the correct command below\n" + "# Write the correct command below\n", + "mv -f ~/DATA/Misc/obits.txt ~/work/OutbreakDetection/Obituaries/" ] }, { @@ -781,7 +814,7 @@ "outputs": [], "source": [ "%%bash\n", - "ls -l /home/jovyan/DATA/Misc" + "ls -l /home/mdsung/DATA/Misc" ] }, { @@ -819,13 +852,13 @@ "This gives the user read, write, and execute permission, the group read permission, and others no permissions\n", "\n", "```bash\n", - "chmod ug:+w home_directory.txt\n", + "chmod ug=+w home_directory.txt\n", "```\n", "\n", "This adds write permission for the user and the group.\n", "\n", "```bash\n", - "chmod a:-w home_directory.txt\n", + "chmod a=-w home_directory.txt\n", "```\n", "\n", "This removes write permissions for all (user, group, other)\n", @@ -851,7 +884,7 @@ "source": [ "## Exercise\n", "\n", - "Copy the ``obits.txt`` file from ``/home/jovyan/DATA/Misc/`` to the ``OutbreakDetection/Obituaries`` directory located in your ``work`` directory. Then change the permissions so that it is read-only for the user, group, and other." + "Copy the ``obits.txt`` file from ``/home/mdsung/DATA/Misc/`` to the ``OutbreakDetection/Obituaries`` directory located in your ``work`` directory. Then change the permissions so that it is read-only for the user, group, and other." ] }, { @@ -860,22 +893,26 @@ "metadata": {}, "outputs": [], "source": [ - "navigating_quizzes.permissions_quiz()" + "%%bash\n", + "cp ~/DATA/Misc/obits.txt ~/work/OutbreakDetection/Obituaries/\n", + "chmod 444 ~/work/OutbreakDetection/Obituaries/obits.txt" ] }, { - "cell_type": "markdown", + "cell_type": "code", + "execution_count": null, "metadata": {}, + "outputs": [], "source": [ - "\"Creative
University of Uah Data Science for Health by Eric Bogenschutz, Thomas Sasani, Brian E. Chapman is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License." + "navigating_quizzes.permissions_quiz()" ] }, { - "cell_type": "code", - "execution_count": null, + "cell_type": "markdown", "metadata": {}, - "outputs": [], - "source": [] + "source": [ + "\"Creative
University of Utah Data Science for Health by Eric Bogenschutz, Thomas Sasani, Brian E. Chapman is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License." + ] } ], "metadata": { @@ -894,7 +931,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.2" + "version": "3.7.3" }, "latex_envs": { "LaTeX_envs_menu_present": true, diff --git a/modules/module1/InClass/pipes.ipynb b/modules/module1/InClass/pipes.ipynb index 0e31858..5c379ef 100644 --- a/modules/module1/InClass/pipes.ipynb +++ b/modules/module1/InClass/pipes.ipynb @@ -59,7 +59,17 @@ "outputs": [], "source": [ "%%bash\n", - "ls -l /home/jovyan/DATA/Misc | grep icd" + "ls -l /home/mdsung/DATA/Misc" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "ls -l /home/mdsung/DATA/Misc | grep icd" ] }, { @@ -77,7 +87,8 @@ "metadata": {}, "outputs": [], "source": [ - "%%bash\n" + "%%bash\n", + "grep \"Oct\\. 17\" /home/mdsung/DATA/Misc/obits.txt | wc -l" ] }, { @@ -86,7 +97,7 @@ "metadata": {}, "outputs": [], "source": [ - "oct_17()" + "oct_17(6)" ] }, { @@ -128,7 +139,8 @@ "metadata": {}, "outputs": [], "source": [ - "%%bash\n" + "%%bash\n", + "grep -ci '[Term]' ~/DATA/Misc/doid.obo" ] }, { @@ -189,7 +201,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module1/InClass/working_in_jupyter.ipynb b/modules/module1/InClass/working_in_jupyter.ipynb index f02a0f5..34a9e55 100644 --- a/modules/module1/InClass/working_in_jupyter.ipynb +++ b/modules/module1/InClass/working_in_jupyter.ipynb @@ -17,14 +17,10 @@ "2. Code cells. Code cells allow us to write and execute code. For the DeCART classes this will be code written in Python (the language from which Juptyer grew), but Juptyer supports many programming languages. You can see a list of supported languages [here](https://github.com/jupyter/jupyter/wiki/Jupyter-kernels).\n", "3. Output cells. Program cells produce output, which for the sake of simplicity I'm going to describe as being a cell.\n", "\n", - "A Markdown cell, a Python code cell, and an output cell are shown below." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Our First Program" + "A Markdown cell, a Python code cell, and an output cell are shown below.\n", + "\n", + "## Our First Program\n", + "\n" ] }, { @@ -73,7 +69,11 @@ }, { "cell_type": "markdown", - "metadata": {}, + "metadata": { + "slideshow": { + "slide_type": "subslide" + } + }, "source": [ "## Working in Notebooks\n", "\n", @@ -85,15 +85,10 @@ "1. How many ways can I add a cell to the notebook?\n", "1. How many ways can I change the order of the cells in the notebook?\n", "1. The program that executes the code in the code cells is called the **kernel**. How can you change which kernel is being used by the notebook? How many different kernels do we have available?\n", - "1. Can you find any interesting ways to change or customize the behavior of the notebooks?" + "1. Can you find any interesting ways to change or customize the behavior of the notebooks?\n", + "\n", + "\n" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { @@ -116,7 +111,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.2" + "version": "3.7.3" }, "latex_envs": { "LaTeX_envs_menu_present": true, diff --git a/modules/module1/ROADMAP.ipynb b/modules/module1/ROADMAP.ipynb index 7bf36ae..f261d70 100644 --- a/modules/module1/ROADMAP.ipynb +++ b/modules/module1/ROADMAP.ipynb @@ -71,7 +71,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.2" + "version": "3.7.3" }, "latex_envs": { "LaTeX_envs_menu_present": true, diff --git a/modules/module2/InClass/Index.ipynb b/modules/module2/InClass/Index.ipynb index 7b6899a..35d64cd 100644 --- a/modules/module2/InClass/Index.ipynb +++ b/modules/module2/InClass/Index.ipynb @@ -42,7 +42,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module2/InClass/remote_data.ipynb b/modules/module2/InClass/remote_data.ipynb index 2f03225..1297d34 100644 --- a/modules/module2/InClass/remote_data.ipynb +++ b/modules/module2/InClass/remote_data.ipynb @@ -36,7 +36,7 @@ "\n", "What we now know as the internet has its roots in the [ARPA Net]() that was designed to exchange data between computers across the country to facilitate decision making regarding potential nuclear attacks. The original ARPA net connected UCLA, UCSB, Stanford, and the University of Utah.\n", "\n", - "![ARPA Net](https://www.sri.com/work/timeline-innovation/images/25_bw_arpanet2.png)\n", + "![ARPA Net](http://3.bp.blogspot.com/-G5GMThbTCPk/VQ1DY5sKMtI/AAAAAAAABv8/Huava5kATbk/w1200-h630-p-k-no-nu/25_bw_arpanet2.png)\n", "\n", "[Various protocols](https://en.wikipedia.org/wiki/Internet_protocol_suite) have been defined for computers to communicate with each other across a network. The most important of these protocols for our purposes are\n", "\n", @@ -107,7 +107,7 @@ "source": [ "## [``curl``](https://curl.haxx.se/docs/manpage.html)\n", "\n", - "``curl`` is a tool similar to ``wget``, but with perhaps more general functionality. Int he following example\n", + "``curl`` is a tool similar to ``wget``, but with perhaps more general functionality. In the following example\n", "\n", "## Example\n", "\n", @@ -118,7 +118,7 @@ "In a terminal type the following command:\n", "\n", "```bash\n", - "curl https://daniel.haxx.se/docs/curl-vs-wget.html | pandoc -S --from=html --to=plain | less\n", + "curl https://daniel.haxx.se/docs/curl-vs-wget.html | pandoc -s --from=html --to=plain | less\n", "```\n", "\n", "## Exercise\n", @@ -208,16 +208,31 @@ "source": [ "## Exercise\n", "\n", - "Make the directories ``/home/jovyan/work/images_wget`` and ``/home/jovyan/images_curl``. Use both ``wget`` and ``curl`` to download the images from ``mynginx`` to the wget and curl directories respectively. Use the ``EXIF.py`` program to answer the following questions:\n", + "Make the directories ``/home/mdsung/work/images_wget`` and ``/home/mdsung/images_curl``. Use both ``wget`` and ``curl`` to download the images from ``mynginx`` to the wget and curl directories respectively. Use the ``EXIF.py`` program to answer the following questions:\n", "\n", - "1. What are the image dimensions of 04.jpg?\n", - "1. What is the date 04.jpg was acquired?\n", - "1. What is the color space of 04.jpg?\n", + "1. What are the image dimensions of 04.jpg? 928 x 928\n", + "1. What is the date 04.jpg was acquired? 2006:08:18 10:07:18\n", + "1. What is the color space of 04.jpg? sRGB\n", "1. What are the image dimensions of ct6.jpg?\n", "1. What is the date ct6.jpg was acquired?\n", "1. What is the color space of ct6.jpg?" ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "cd ~/work/image_curl/; curl web_server/imgs/bigneck.jpg -o bigneck.jpg\n", + "cd ~/work/image_wget/; wget web_server/imgs/bigneck.jpg\n", + "cd ~/work/image_curl/; curl web_server/imgs/04.jpg -o 04.jpg\n", + "cd ~/work/image_wget/; wget web_server/imgs/04.jpg\n", + "cd ~/work/image_curl/; curl web_server/imgs/ct6.jpg -o ct6.jpg\n", + "cd ~/work/image_wget/; wget web_server/imgs/ct6.jpg" + ] + }, { "cell_type": "markdown", "metadata": {}, @@ -248,7 +263,19 @@ "execution_count": null, "metadata": {}, "outputs": [], - "source": [] + "source": [ + "%%bash\n", + "\n", + "cd ../../../../work/images_wget/\n", + "pwd" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "![A 3D rendering of a CTA of neck](../../../../work/images_wget/bigneck.jpg)" + ] } ], "metadata": { @@ -267,7 +294,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module2/InClass/ssh_scp.ipynb b/modules/module2/InClass/ssh_scp.ipynb index 8c4846e..668147c 100644 --- a/modules/module2/InClass/ssh_scp.ipynb +++ b/modules/module2/InClass/ssh_scp.ipynb @@ -50,10 +50,10 @@ "\n", "We use ``ssh`` to connect to a remote computer. For example, I frequently connect from my laptop to a workstation in my office. Another important application would be connecting to a server in the cloud, for example a server you have setup with [Amazon Web Services](https://aws.amazon.com/free/?sc_channel=PS&sc_campaign=acquisition_US&sc_publisher=google&sc_medium=cloud_computing_b&sc_content=aws_url_e_control_q32016&sc_detail=amazon.%20web%20services&sc_category=cloud_computing&sc_segment=188908164667&sc_matchtype=e&sc_country=US&s_kwcid=AL!4422!3!188908164667!e!!g!!amazon.%20web%20services&ef_id=WVKaPAAAAfUJDrqI:20170627174740:s). \n", "\n", - "For this course, we have set up a remote server called ``myssh``. To connect to this server, we will open a terminal and type the command\n", + "For this course, we have set up a remote server called ``ssh_server``. To connect to this server, we will open a terminal and type the command\n", "\n", "```bash\n", - "ssh myssh\n", + "ssh ssh_server\n", "```\n", "\n", "![initial ssh](../../../media/ssh2.png)\n", @@ -118,7 +118,7 @@ "\n", "```bash\n", "\n", - "scp jovyan@myssh:/home/jovyan/chapman_brian/timestamp.txt .\n", + "scp jovyan@ssh_server:/home/jovyan/mdsung/timestamp.txt .\n", "```\n", "Edit the directory name to match your directory." ] @@ -323,7 +323,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module2/InClass/vi.ipynb b/modules/module2/InClass/vi.ipynb index b60bee7..a9b2001 100644 --- a/modules/module2/InClass/vi.ipynb +++ b/modules/module2/InClass/vi.ipynb @@ -125,9 +125,9 @@ "\n", "Navigate and search through the document to answer the following questions:\n", "\n", - "1. On what line is the ``DOID`` for a renal Wilms' tumor defined?\n", - "1. What is the name of the term defined two terms after \"generalized anxiety disorder\" is defined?\n", - "1. What is the name of the parent term for a melanoma (DOID:1909)?" + "1. On what line is the ``DOID`` for a renal Wilms' tumor defined? 52488\n", + "1. What is the name of the term defined two terms after \"generalized anxiety disorder\" is defined? Plasmodium malariae malaria\n", + "1. What is the name of the parent term for a melanoma (DOID:1909)? cutaneous fibrohistiocytic neoplasm" ] }, { @@ -199,7 +199,11 @@ "execution_count": null, "metadata": {}, "outputs": [], - "source": [] + "source": [ + "%%bash\n", + "ls -l *.txt\n", + "pwd" + ] } ], "metadata": { @@ -218,7 +222,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module2/InClass/viewing_files.ipynb b/modules/module2/InClass/viewing_files.ipynb index 3b28c4c..687e3f9 100644 --- a/modules/module2/InClass/viewing_files.ipynb +++ b/modules/module2/InClass/viewing_files.ipynb @@ -55,7 +55,7 @@ "outputs": [], "source": [ "%%bash\n", - "cat /home/jovyan/DATA/Misc/obits.txt" + "cat /home/mdsung/DATA/Misc/obits.txt" ] }, { @@ -72,7 +72,7 @@ "outputs": [], "source": [ "%%bash\n", - "cat /home/jovyan/DATA/Misc/obits.txt /home/jovyan/DATA/README.txt" + "cat /home/mdsung/DATA/Misc/obits.txt /home/mdsung/DATA/README.txt" ] }, { @@ -114,8 +114,8 @@ "metadata": {}, "outputs": [], "source": [ - "from viewing_quizzes import *\n", - "oct15(ocount=-1)" + "%%bash\n", + "grep \"Oct. 15\" /home/mdsung/DATA/Misc/obits.txt |wc -l" ] }, { @@ -123,7 +123,10 @@ "execution_count": null, "metadata": {}, "outputs": [], - "source": [] + "source": [ + "from viewing_quizzes import *\n", + "oct15(ocount=6)" + ] } ], "metadata": { @@ -142,7 +145,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module2/ROADMAP.ipynb b/modules/module2/ROADMAP.ipynb index 2572473..32d02ec 100644 --- a/modules/module2/ROADMAP.ipynb +++ b/modules/module2/ROADMAP.ipynb @@ -88,7 +88,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/modules/module3/InClass/compression.ipynb b/modules/module3/InClass/compression.ipynb index 187f7f1..84602b3 100644 --- a/modules/module3/InClass/compression.ipynb +++ b/modules/module3/InClass/compression.ipynb @@ -93,7 +93,7 @@ "outputs": [], "source": [ "import compression_quizzes as cq\n", - "cq.examine_img(\"/home/jovyan/DATA/Images/PE/Ser_000006/IM-0124-0097.dcm\")" + "cq.examine_img(\"/home/mdsung/DATA/Images/PE/Ser_000006/IM-0124-0097.dcm\")" ] }, { @@ -135,7 +135,7 @@ "outputs": [], "source": [ "import PIL\n", - "fname = \"/home/jovyan/work/nci/04\"\n", + "fname = \"/home/mdsung/work/image_wget/04\"\n", "for q in range(100, 0, -10):\n", " PIL.Image.open(fname+\".jpg\").save(\"%s_%03d.jpg\"%(fname,q), quality=q)\n", "# Save a TIFF for reference\n", @@ -311,9 +311,7 @@ "```bash\n", "tar cvfz ~/Modules.tgz Modules\n", "```\n", - "\n", "Same as the command above, but compresses the archive with ``gzip``.\n", - "\n", "```bash\n", "\n", "tar cvfz ~/notebooks.tgz `find ./Modules -name '*.ipynb'`\n", @@ -380,7 +378,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.2" + "version": "3.7.3" } }, "nbformat": 4,