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image: alpine:latest
pages:
stage: deploy
script:
- echo 'Nothing to do...'
artifacts:
paths:
- public
only:
- main
README.md
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......@@ -4,4 +4,12 @@ Everything needed to prepare the Data Science Journal Club (DSJC) Course on Canv
## Syllabus
To obtain the latest copy of the syllabus, please go [here](https://gitlab.rc.uab.edu/rc-data-science/communications/dsjc-course/-/blob/main/data_science_journal_club_syllabus.html) and click the download button on the far right, just above the code. Looks like a downward facing arrow point into an inbox.
### Release Version
**USE ME**
Release version presented as a static webpage [here](https://s3.lts.rc.uab.edu/uab-rc-dsjc/syllabus.html)
### Development Version
Development version [here](https://gitlab.rc.uab.edu/rc-data-science/communications/dsjc-course/-/blob/main/data_science_journal_club_syllabus.html). Click the download button on the far right, just above the code. Looks like a downward facing arrow point into an inbox.
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# DSJC New Session Checklist
The course is a collaboration between Kristina Visscher of the UAB Department of Neurobiology and UAB IT Research Computing. The intent of the course is to provide a guided platform for self-motivated students to learn more about Data Science and its important accessory skills. Accessory skills include software development, programming, data engineering, image and signal processing, visualization development, and high performance computing.
The course runs every session each year: Fall, Spring, Summer. The UAB Academic Calendar dictates when classes start for each session. As instructors, our goal should be to have the course published the week before classes start.
## Course Setup Checklist
### Instructor of Record
- [ ] Merge GBSC and IDNE sections.
- Must be done by [IOR](#abbreviations).
- Please visit [Canvas: Course Cross-Listing SLA page](https://uabprod.service-now.com/service_portal?id=sc_cat_item&sys_id=393e9275377d630024a67c1643990e27).
- [ ] Add course Teachers and Instructors as needed.
- Must be done by [IOR](#abbreviations) _after_ merge step is complete! Otherwise, adds may need to be redone.
- Please visit [Canvas: Add/Remove User(s) SLA page](https://uabprod.service-now.com/service_portal?id=sc_cat_item&sys_id=76f97b59374a670024a67c1643990ece).
- Teacher/Instructor List:
- `wwarr` for William Warriner
- `mdefende` for Matt Defenderfer
- `prema` for Prema Soundararajan
### Teachers/Other Instructors
- [ ] Set up the Syllabus Affirmation Assignment
1. Navigate to Quizzes page.
2. Click "+ Quiz" button.
3. Select "Classic Quizzes".
4. Click "Submit" button.
5. Enter in first text entry box: `Syllabus Affirmation`.
6. Enter in the "Quiz Instructions" text entry box:
> "In a new window, please read the Syllabus, then return here to complete the affirmation."
7. Create a link to the Syllabus Course Page at the word "Syllabus" in the previous step.
8. Set the following field values in the remainder of the form.
- Quiz Type: `Graded Quiz`
- Assignment Group: `Assignments`
- Options:
- Shuffle Answers: `checked`
- Time Limit: `unchecked`
- Allow Multiple Attempts: `checked`
- Quiz Score to Keep: `highest`
- Allowed Attempts: `unchecked`
- Let Students See Their Quiz Responses: `checked`
- Only Once After Each Attempt: `checked`
- Let Students See The Correct Answers: `unchecked`
- Show one question at a time: `unchecked`
- Quiz Restrictions:
- Require an access code: `unchecked`
- Filter IP Addresses: `unchecked`
- Assign:
- Assign to: `Everyone`
- Due: Wednesday of 2nd week.
- Available from/until: both blank
9. Click "Questions" tab.
10. Click "+ New Question".
- In the top-left Text Entry box enter "First Demonstration Due Date"
- In the Drop Down box select "Multiple Choice"
- Enter the text "When is the first demonstration due?" in the main text entry box.
- Make one answer the correct date (see the Syllabus for timings).
- Make other answers other dates.
- Click "Update Question".
11. Click "Details" tab.
12. Click "Save & Publish" button.
- [ ] Set up the [Demonstration Assignment HTML](demonstration_assignment.html)
1. Navigate to Assignments page.
2. Click "+ Assignment" button.
3. Enter Assignment Name in text entry box: `Demonstration #1`.
4. Switch text entry box to raw HTML mode by clicking `</>` symbol at bottom-right of box.
5. Copy-paste [HTML](demonstration_assignment.html) into text entry box.
6. Update Syllabus link.
1. On the first line is HTML tag that looks like `<a title="Syllabus" href="">`.
2. Copy-paste Syllabus Page URL between double quotes after `href=`.
7. Make any other necessary changes to the assignment HTML. Don't forget to update in the repository!
8. Switch to WYSIWYG mode: click `</>` symbol again.
9. Set the following field values in the remainder of the form.
- Points: `1`
- Assignment Group: `Assignments`
- Display Grade as: `Complete/Incomplete`
- Submission Type: `No Submission`
- Group Assignment: unchecked
- Peer Reviews: unchecked
- Assign:
- Assign to: `Everyone`
- Due: **varies, see table below**
Assignment due dates should be staggered, with at least three weeks between them, always on a Friday. The following table contains due dates for each. You will need to determine the actual calendar dates for each semester. Be sure to account for Spring Break in the Spring semester! Don't let assignments land on holidays or break days.
| Session Length | #1 Due Date | #2 Due Date | #3 Due Date |
| -------------- | ----------- | ----------- | ----------- |
| 14 weeks | 6th week | 10th week | 14th week |
| 10 weeks | 4th week | 7th week | 10th week |
- Available from/until: blank
10. Click save and publish!
11. For `Demonstration #2` and `Demonstration #3`:
1. Go to the main Assignments page.
2. Click the vertical three dots next to the `Demonstration #1` assignment you created.
3. Click "Duplicate".
4. On the new entry, click the vertical three dots, then "Edit Assignment".
5. Modify the "Name" field appropriately.
6. Click "Save & Publish".
12. Verify the assignments are published in the Assignments main page, with a green checkmark icon next to each.
- [ ] Upload [Syllabus HTML](syllabus.html)
1. Navigate to Syllabus page.
2. Switch text entry box to raw HTML mode by clicking `</>` symbol at bottom-right of box.
3. Copy-paste [HTML](syllabus.html) into text entry box.
4. Update Syllabus Affirmation assignment link.
1. Look for the HTML tags like `<a title="Syllabus Affirmation" href="">`.
2. For each one, add the appropriate assignment page path, which should look like `/courses/$course_number/quizzes/$quiz_number`, e.g. like `/courses/1601187/assignments/2325855`. This can be found by visiting the assignment to get the `$course_number` and `$assignment_number` values.
3. Only the trailing part of the URL starting with `/courses` is needed. The leading `/` is required.
5. Update Demonstration assignment links.
1. Look for the three HTML tags like `<a title="Demonstration #1" href="">`.
2. For each one, add the appropriate assignment page path, which should look like `/courses/$course_number/assignments/$assignment_number`, e.g. like `/courses/1601187/assignments/6860919`. This can be found by visiting the assignment to get the `$course_number` and `$assignment_number` values.
3. Only the trailing part of the URL starting with `/courses` is needed. The leading `/` is required.
6. Switch to WYSIWYG mode: click `</>` symbol again.
7. Check "Show Course Summary" checkbox.
8. Verify formatting is correct.
9. Update syllabus at <https://s3.lts.rc.uab.edu/uab-rc-dsjc/syllabus.html> by manual upload.
- [ ] Set up Home page.
1. Navigate to Home page.
2. Click "Choose Home Page" button.
3. Select "Syllabus".
- [ ] Set up Settings page.
- Navigation tab:
- Disable all except:
- Home
- Announcements
- Syllabus
- Assignments
- Grades
- People
- UAB Cares
- UAB Policies
- UAB Libraries
- Technology Resources
- Student Academic and Support Services
- Put them in the above order!
- Click Save when done.
- [ ] Verify links using "Validate Links in Content" on Settings page.
- Note: `https://rc.uab.edu` may be marked as unreachable. Double check that it works correctly manually. This should be a false positive.
- [ ] Use Student View to verify the course has appropriate appearance and function.
- Make sure syllabus looks correct.
- Make sure assignments are visible (they need to be published individually).
- [ ] Publish the course. May need to be done by IOR.
- [ ] Make an announcement welcoming new students.
1. Navigate to Announcements Page.
2. Click `+ Announcements` button.
3. Enter Topic Title as "Welcome to the Data Science Journal Club course!"
4. Switch text entry box to raw HTML mode by clicking `</>` symbol at bottom-right of box.
5. Copy-paste [HTML](welcome_announcement.html) into text entry box.
6. Switch to WYSIWYG mode: click `</>` symbol again.
7. Modify as necessary to be relevant to the current session.
## Important Information
### People
| Course Title | UAB Title | Name | email |
| :------------------- | :--------------------------- | :------------------- | :----------------- |
| Instructor of Record | Associate Professor | Kristina M. Visscher | <kmv@uab.edu> |
| Instructor | RC Facilitation Manager | William Warriner | <wwarr@uab.edu> |
| Instructor | RC Facilitator (Scientist I) | Matthew Defenderfer | <mdefende@uab.edu> |
| Instructor | RC Facilitator (Scientist I) | Prema Soundararajan | <prema@uab.edu> |
### Relevant Pages
- UAB Academic Calendar: <https://www.uab.edu/students/academics/academic-calendar>
### Abbreviations
- **DSJC**: Data Science Journal Club
- **GBSC**: Graduate Biomedical Sciences
- **IDNE**: Neuroengineering
- **IOR**: Instructor of Record
- **RC**: Research Computing
- **SLA**: Service Level Agreement
- **TA**: Teaching Assistant
- **WYSIWYG**: What You See Is What You Get
- Refers to a kind of text editor that lets you see what the resulting document will look like as you make changes.
- Microsoft Word is WYSIWYG.
- Most Canvas Page text entry boxes are WYSIWYG by default.
## Notes on Using Canvas
Most Canvas Page text entry boxes, including those of Syllabus and Assignments, have a WYSIWYG HTML editor. The entry mode can be changed to raw HTML mode by clicking the `</>` symbol at the bottom-right of the box. We use raw HTML mode extensively, allowing us to version control invidividual pages for the content of the course.
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<p>Bear in mind objectives and resources from the <a title="Syllabus" href="">Syllabus</a>:</p>
<ol start="1" type="1">
<li>Learn new data science stuff</li>
<li>Grapple with that new stuff</li>
<li>Discuss that new stuff with us</li>
</ol>
<p>Data Science Club Material to get you started: <a class="external"
href="https://www.youtube.com/channel/UCZoOS2e699Ge0DND1oy1BJQ" target="_blank"
rel="noopener"><span>https://www.youtube.com/channel/UCZoOS2e699Ge0DND1oy1BJQ</span></a>. Feel free to use other
sources, please inform us of those sources.</p>
<p>Office Hours are held Mondays and Thursdays from 10 AM to noon via Zoom. Meeting links are available at <a
class="inline_disabled" href="https://docs.rc.uab.edu/#contact-us" target="_blank"
rel="noopener noreferrer">https://docs.rc.uab.edu/#contact-us</a>.</p>
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# DSJC New Session Checklist
The intent is to have the course run every session each year: Fall, Spring, Summer. The UAB Academic Calendar dictates when classes start for each session, and the goal should be to have the course published the week before classes start.
Instructor of Record: Kristina M. Visscher <mailto:kmv@uab.edu>
UAB Academic Calendar: <https://www.uab.edu/students/academics/academic-calendar>
## The Checklist
- [ ] Merge GBSC and IDNE sections. Requires a ticket via course instructor Kristina Visscher <mailto:kmv@uab.edu>.
- [ ] Add course TAs and instructors as needed. Requires a ticket via course instructor Kristina Visscher <mailto:kmv@uab.edu>. This must occur _after_ the merger! Please instruct central IT on this point.
- [ ] Upload the [syllabus](data_science_journal_club_syllabus.html)
- Click the `</>` symbol at the bottom-right of the big text box and copy-paste the HTML (linked above) into the box. Click the symbol again to verify the formatting is correct.
- Show Course Summary: checked
- **Manually verify all links!**
- [ ] Set up the [assignments](data_science_journal_club_assignment.html)
- Assignment name e.g. `Demonstration #1`
- Click the `</>` symbol at the bottom-right of the big text box and copy-paste the HTML (linked above) into the box. Click the symbol again to verify the formatting is correct.
- **Change the "Syllabus" link to the new course syllabus URL.**
- Points: `1`
- Display Grade as: `Complete/Incomplete`
- Submission Type: `No Submission`
- Group Assignment: unchecked
- Peer Reviews: unchecked
- Assign:
- Assign to: Everyone
- Due: last day of final exams according to the current session on <https://www.uab.edu/students/academics/academic-calendar>
- Available from/until: blank
- Click save and publish! Ensure the assignments are published in the Assignments main page, with a green checkmark icon next to each.
Once the first one is created, go to the main Assignments page. Click the vertical three dots next to the assignment you created. Click "Duplicate" and go from there.
- **Manually verify all links!**
- [ ] Adjust settings
- Course Details tab:
- Set appropriate start and end dates according to <https://www.uab.edu/students/academics/academic-calendar>
- End date should be at least one week after the last day of final exams so students may review their grades and course material
- Typically Canvas does a good job of picking these dates
- Navigation tab:
- Disable all except:
- Home
- Announcements
- Syllabus
- Assignments
- Grades
- People
- Chat
- UAB Libraries
- UAB Cares
- UAB Policies
- Technology Resources
- Student Academic and Support Services
- Put them in the above order
- [ ] Use Student View to verify the course has appropriate appearance and function.
- Make sure syllabus looks good
- Make sure assignments are visible (they need to be published)
- **Manually verify all links!**
- [ ] Publish the course. Requires the help of instructor Kristina Visscher <mailto:kmv@uab.edu>.
- [ ] Make an announcement welcoming new students.
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<h2 id="top_">SP2023 GBSC/IDNE 720/790-VTR JC- Data Science Club</h2>
<p>Welcome!</p>
<p>The Data Science Journal Club course comes from a collaboration between the UAB IT Research Computing (RC) group, the
Graduate Biomedical Sciences (GBSC) department and the Neuroengineering (IDNE) department. The course exists to
foster knowledge transfer between Research Computing and students interested in growing their data science,
programming and high-performance computing skill set. Future years will see increasing demand for these skills in
every employment sector. Our goal is to enable students to be more competitive in their future careers by
facilitating self-directed growth in the data science space. We accept students at all skill levels of data science,
assuming familiarity with computers and graphical plots.</p>
<p>While the course is mostly self-directed and hands-off, we don't want students to get lost. We want you to be
successful and come away from this course feeling confident in applying the skills you have learned. If you have
concerns, get stuck, need ideas or even a <a href="https://en.wikipedia.org/wiki/Rubber_duck_debugging">rubber
duck</a>, please feel free to contact us.</p>
<p>&nbsp;</p>
<p>Please take the time to read this syllabus in its entirety. All of the information here should be useful as you work
through the course.<a href="http://www.uab.edu/dss"></a></p>
<p>&nbsp;</p>
<h3 id="dei">Diversity, Equity and Inclusion (DEI) Statement:</h3>
<p>The University of Alabama at Birmingham considers the diversity of its students, faculty, and staff to be a strength
and critical to its educational mission. We will strive to be an inclusive community where we can learn from the
many perspectives and worldviews which may differ from our own. We are all expected to contribute to creating a
respectful, welcoming, and safe environment that fosters a sense of belonging through open and honest dialogue. To
this end, we will conduct discussions in a way that honors, respects, and extends dignity to everyone.</p>
<p>Please visit <a class="inline_disabled" href="https://www.uab.edu/dei/" target="_blank"
rel="noopener">https://www.uab.edu/dei/</a> for more information.</p>
<p>&nbsp;</p>
<h3 id="intent">Our Intent:<strong><br /></strong></h3>
<p>Our intent with the course has three parts. The first is for students to learn new techniques and technologies to
assist with or facilitate data science. The second is for students to grapple with the application of those
techniques and technologies. The third is to discuss with us how that went so we can check understanding and provide
mentoring and guidance. We also love seeing all the cool stuff our students learn, and frequently find ourselves
learning new perspectives, details, gotchas and technologies in the process.</p>
<p>To summarize students will:</p>
<ol start="1" type="1">
<li>Learn new data science related stuff</li>
<li>Grapple with that new stuff</li>
<li>Discuss that new stuff with us</li>
</ol>
<p>&nbsp;</p>
<h3 id="work">Required Work:</h3>
<p>All students are required to give three demonstrations<strong></strong></p>
<ul>
<li>during any office hours, one per visit...</li>
<li>...in a student-led informal discussion style.</li>
<li>Students may collaborate on projects...</li>
<li>...but each student must show their original work.</li>
<li>Each demonstration must be data science related or somehow facilitate data science.</li>
</ul>
<p>We realize the last bullet point is very broad, so we account for student knowledge, skill and experience when you
give your demonstrations. We have no expectations of student starting skill level or experience. With that in mind,
examples of past topics are included in the following list. If you have an idea but are unsure if it would be
sufficient material, please feel free to contact us.</p>
<ul>
<li>Using machine learning or deep learning to create a predictive model.</li>
<li>Creating your very first Anaconda environment to share with collaborators.</li>
<li>Learning to use version control (git and github) with your existing code.</li>
<li>Extracting insights from existing results by applying new visualization methods.</li>
<li>Migrating a data analysis workflow from Excel to Python and pandas.</li>
<li>Scaling a data analysis workflow from a lab workstation to Cheaha.</li>
<li>Exploring a new programming language.</li>
<li>Writing your very first script in any programming language.</li>
<li>Identifying and extracting salient features from complex data for further processing.</li>
<li>Understand what makes data tidy and why it is important.</li>
</ul>
<p>As you prepare for your demonstrations, please be thinking about the context of your work. An incomplete list of
questions to guide your thoughts about context.</p>
<ul>
<li>What are some drawbacks or limitations?</li>
<li>How does it compare to alternatives?</li>
<li>How does it work?</li>
<li>Why does it work?</li>
<li>Where can we go next?</li>
<li>Why will others want to use my work?</li>
<li>How can I transfer techniques to other projects?</li>
</ul>
<p>Be prepared for us to challenge you with new ways of thinking!</p>
<p><strong>We are less interested in what your results are, and more interested in how you obtained those results and
how they fit into the context of data science in general and your field in particular.<br /></strong></p>
<p>If you are not able to make the office hours sessions, please contact us as soon as possible to make alternative
arrangements.</p>
<p><strong>The dates in the course summary below are the last day of final exams, and therefore the due dates for the
demonstrations. Please plan ahead to finish all three of them before that date. We cannot accept work after the
due dates below without prior, individual discussion.<br /></strong></p>
<p>&nbsp;</p>
<h3 id="grading">Grading:</h3>
<p>The course is pass/fail. Grading is based purely on attendance and demonstrations. Three demonstrations are required,
each has its own assignment within Canvas.</p>
<p>The demonstrations are all due by the end of the session (i.e. Fall, Spring, Summer). Because office hours are open
to potentially hundreds of researchers outside the scope of this course, <strong>only one session can be presented
per student per office hours visit.</strong> <strong><em>Please plan accordingly.</em></strong></p>
<p>If for any reason you are not able to adhere to the above requirements, please contact us as soon as you know so we
can make plans to accommodate you. Remember, we want you to be successful!</p>
<h3 id="scheduling">Scheduling, Attendance &amp; Office Hours:</h3>
<p>Our course may differ from the typical university course experience. We do not host regularly scheduled course
meetings. Instead, we offer twice-weekly office hours. The office hours serve two purposes for this course.</p>
<ol style="list-style-type: decimal;">
<li>Each student must make three office hours visits for the three demonstrations.</li>
<li>Students are encouraged to attend office hours if they have questions that are best answered in a virtual
meeting. Past examples include:</li>
</ol>
<ul>
<li style="list-style-type: none;">
<ul style="list-style-type: disc;">
<li>Is my topic suitable for this course?</li>
<li>Where can I find more resources on topics?</li>
<li>Can you preview my demonstration material?</li>
<li>Am I on the right track?</li>
</ul>
</li>
</ul>
<p>Office Hours are held Mondays and Thursdays from 10 AM to noon via Zoom. Meeting links are available at our
documentation (<a href="https://docs.rc.uab.edu/#contact-us" target="_blank"
rel="noopener">https://docs.rc.uab.edu/#contact-us</a>).</p>
<p>&nbsp;</p>
<h3 id="resources">Course Resources:</h3>
<p>For students who are just entering the data science space, please consider trying some of Kaggle's micro-courses on
data analysis, visualization and machine learning: <a class="inline_disabled" href="https://www.kaggle.com/learn"
target="_blank" rel="noopener">https://www.kaggle.com/learn</a>.</p>
<p>For students who want to develop skills to facilitate data science, see the Software Carpentry's list of lessons: <a
class="inline_disabled" href="https://software-carpentry.org/lessons/" target="_blank"
rel="noopener">https://software-carpentry.org/lessons/</a>. These lessons include the Unix shell, Git version
control and programming skills in Python and R.</p>
<p>For students who want to develop data literacy skills in the context of specific fields, see the Data Carpentry's
list of lessons: <a class="inline_disabled" href="https://datacarpentry.org/lessons/" target="_blank"
rel="noopener">https://datacarpentry.org/lessons/</a>. One of the included fields is genomics, which may be of
particular interest to many UAB students.</p>
<p>For students interested in learning more about any of the above with a focus on scaling with high-performance
computing, we maintain a YouTube channel with some Data Science Club Material to get you started using Cheaha: <a
class="external" href="https://www.youtube.com/channel/UCZoOS2e699Ge0DND1oy1BJQ" target="_blank"
rel="noopener"><span>https://www.youtube.com/channel/UCZoOS2e699Ge0DND1oy1BJQ</span></a>.</p>
<p>Feel free to seek out and use other sources! If you do so, please inform us of those sources so we can curate our
list and better serve future students.</p>
<p>&nbsp;</p>
<h3 id="support">Technical Support:</h3>
<p>Research Computing Official Site: <a class="external" href="https://www.uab.edu/it/home/research-computing"
target="_blank" rel="noopener">https://www.uab.edu/it/home/research-computing</a>.</p>
<p>Cheaha Documentation: <a class="external" href="https://docs.rc.uab.edu" target="_blank"
rel="noopener">https://docs.rc.uab.edu</a>.</p>
<p>Cheaha Web Portal: <a class="external" href="https://rc.uab.edu" target="_blank"
rel="noopener">https://rc.uab.edu</a>.</p>
<p>If you need software installed, or something just doesn't work like you expect, please email us at <a
href="mailto:support@listserv.uab.edu" target="_blank" rel="noopener">support@listserv.uab.edu</a>. When asking
for help, consider including all relevant details about your goal, what you tried, what you expected to happen, what
actually happened, steps needed to reproduce the issue, and any error messages. If the error messages are longer
than about 10 lines, copy-paste them into a text document and attach that to the email instead. Screenshots are also
helpful. See our documentation on support (<a href="https://docs.rc.uab.edu/help/support" target="_blank"
rel="noopener">https://docs.rc.uab.edu/help/support</a>) for more information.</p>
<p>&nbsp;</p>
<h3 id="dss">Disability Support Services (DSS) Statement<strong>:<br /></strong></h3>
<p>UAB is committed to providing an accessible learning experience for all students. If you are a student with a
disability that qualifies under the Americans with Disabilities Act (ADA) and/or Section 504 of the Rehabilitation
Act, and you require accommodations, please contact Disability Support Services for information on accommodations,
registration and procedures. Requests for reasonable accommodations involve an interactive process and consist of a
collaborative effort among the student, DSS, faculty and staff. If you are registered with Disability Support
Services, please contact me to discuss accommodations that may be necessary in this course. If you have a disability
but have not contacted Disability Support Services, please call 934-4205 or visit <a
href="http://www.uab.edu/dss">http://www.uab.edu/dss</a>.</p>
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<p>Hello everyone and welcome to Data Science Journal Club (DSJC)!</p>
<p>Please take a few minutes to read over the <a title="Syllabus"
href="/courses/1593764/assignments/syllabus">syllabus</a> as it is the central repository for information about
this course.</p>
<p>If you are new to the course, welcome! We hope you have an enlightening experience. We are happy to answer questions
and provide guidance, please feel free to reach out with questions, and please read the syllabus for more detailed
information about expectations.</p>
<p>If you are returning, welcome back! Not much has changed this time around other than a slightly updated syllabus.</p>
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<p>Bear in mind objectives and resources from the <a title="Syllabus" href="">Syllabus</a>:</p>
<ol start="1" type="1">
<li>Learn new data science stuff</li>
<li>Grapple with that new stuff</li>
<li>Discuss that new stuff with us at Office Hours</li>
</ol>
<p>Office Hours are held Mondays and Thursdays from 10 AM to noon via Zoom. Meeting links are available at <a class="inline_disabled" href="https://docs.rc.uab.edu/#how-to-contact-us" target="_blank" rel="noopener noreferrer">https://docs.rc.uab.edu/#how-to-contact-us</a>.</p>
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<h2 id="top_">SP2024 GBSC/IDNE 720/790-VTR JC- Data Science Club</h2>
<p>Welcome!</p>
<p>The Data Science Journal Club course comes from a collaboration between the UAB IT Research Computing (RC) group, the Graduate Biomedical Sciences (GBSC) department and the Neuroengineering (IDNE) department. The course exists to foster knowledge transfer between Research Computing and students interested in growing their data science, programming and high-performance computing skill set. Future years will see increasing demand for these skills in every employment sector. Our goal is to enable students to be more competitive in their future careers by facilitating self-directed growth in the data science space. We accept students at all skill levels of data science, assuming familiarity with computers and graphical plots.</p>
<p>While the course is mostly self-directed and hands-off, we don't want students to get lost. We want you to be successful and come away from this course feeling confident in applying the skills you have learned. If you have concerns, get stuck, need ideas or even a <a href="https://en.wikipedia.org/wiki/Rubber_duck_debugging">rubber duck</a>, please feel free to contact us.</p>
<p>&nbsp;</p>
<p>Please take the time to read this syllabus in its entirety. All of the information here should be useful as you work through the course.</p>
<p>&nbsp;</p>
<h3>Instructor Information:</h3>
<p>Course Instructors (please contact us first!)</p>
<p>William Warriner (he/him), <a href="mailto:wwarr@uab.edu" target="_blank" rel="noopener">wwarr@uab.edu</a></p>
<p>Matthew Defenderfer, <a href="mailto:mdefende@uab.edu" target="_blank" rel="noopener">mdefende@uab.edu</a></p>
<p>Prema Soundararajan, <a href="mailto:prema@uab.edu" target="_blank" rel="noopener">prema@uab.edu</a></p>
<p>Office Hours information is available here: <a class="inline_disabled" href="https://docs.rc.uab.edu/#how-to-contact-us" target="_blank" rel="noopener">https://docs.rc.uab.edu/#how-to-contact-us</a></p>
<p>&nbsp;</p>
<p>Instructor of Record (please contact only as a last resort!)</p>
<p>Kristina Visscher, <a href="mailto:kmv@uab.edu" target="_blank" rel="noopener">kmv@uab.edu</a></p>
<p>&nbsp;</p>
<h3 id="oae">Office of Access and Engagement:</h3>
<p>The Office of Access & Engagement works to promote success for everyone in the UAB community. We work to address challenges faced by our students, faculty and staff to ensure everyone has access to available programs and resources they need to promote success and retention, and to foster an accessible and welcoming culture.</p>
<p>Since its founding, UAB has played a pivotal role in shaping the future in Birmingham and beyond by making a positive difference in as many lives as possible. We do this by serving all people — a commitment that continues today through our vision, mission and shared values.</p>
<p>The Office of Access & Engagement strives to make sure every member of the UAB community has access to available programs and resources they need, recognizing that some students, faculty and staff may face more barriers and have a greater need for additional support than others due to their circumstances.</p>
<p>Please visit <a class="inline_disabled" href="https://www.uab.edu/access-engagement/students" target="_blank" rel="noopener">The Office of Access and Engagement Website</a> for more information.</p>
<p>&nbsp;</p>
<h3 id="intent">Course Intent:<strong><br /></strong></h3>
<p>Our intent with the course has three parts. The first is for students to learn new techniques and technologies to assist with or facilitate data science. The second is for students to grapple with the application of those techniques and technologies. The third is to discuss with us how that went so we can check understanding and provide mentoring and guidance. We also love seeing all the cool stuff our students learn, and frequently find ourselves learning new perspectives, details, gotchas and technologies in the process.</p>
<p>To summarize students will:</p>
<ol start="1" type="1">
<li>Learn new data science related stuff</li>
<li>Grapple with that new stuff</li>
<li>Discuss that new stuff with us</li>
</ol>
<p>&nbsp;</p>
<h3 id="work">Required Work:</h3>
<p>All students are required to give three demonstrations<strong></strong></p>
<ul>
<li>during any office hours, one per visit...</li>
<li>...in a student-led informal discussion style.</li>
<li>Students may collaborate on projects...</li>
<li>...but each student must show their original work.</li>
<li>Each demonstration must be data science related or somehow facilitate data science.</li>
</ul>
<p>We realize the last bullet point is very broad. This is intentional as we account for student knowledge, skill and experience when you give your demonstrations. We have no expectations of student starting skill level or experience. With that in mind, examples of past topics are included in the following list. If you have an idea but are unsure if it would be sufficient material, please feel free to contact us.</p>
<ul>
<li>Using machine learning or deep learning to create a predictive model.</li>
<li>Creating your very first Anaconda environment to share with collaborators.</li>
<li>Learning to use version control (git and github) with your existing code.</li>
<li>Extracting insights from existing results by applying new visualization methods.</li>
<li>Migrating a data analysis workflow from Excel to Python and pandas.</li>
<li>Scaling a data analysis workflow from a lab workstation to Cheaha.</li>
<li>Exploring a new programming language.</li>
<li>Writing your very first script in any programming language.</li>
<li>Identifying and extracting salient features from complex data for further processing.</li>
<li>Understand what makes data tidy and why it is important.</li>
</ul>
<p>As you prepare for your demonstrations, please be thinking about the context of your work. An incomplete list of questions to guide your thoughts about context.</p>
<ul>
<li>What are some drawbacks or limitations?</li>
<li>How does it compare to alternatives?</li>
<li>How does it work?</li>
<li>Why does it work?</li>
<li>Where can we go next?</li>
<li>Why will others want to use my work?</li>
<li>How can I transfer techniques to other projects?</li>
</ul>
<p>Be prepared for us to challenge you with new ways of thinking!</p>
<p><strong>We are less interested in what your results are, and more interested in how you obtained those results and how they fit into the context of data science in general and your field in particular.<br /></strong></p>
<p>If you are not able to make the office hours sessions, please contact us as soon as possible to make alternative arrangements.</p>
<p><strong>The date of the final Demonstration in the course summary below is the last day of final exams, and therefore the final due date for all work. Please plan ahead to finish all assignments before that date. We cannot accept work after the due dates below without prior, individual discussion.<br /></strong></p>
<p>&nbsp;</p>
<h3 id="grading">Grading:</h3>
<p>The course is treated as a pass/fail course. The grade reflected on your transcript may depend on the section you are in. If the section you are in uses a letter grade, then a pass is assigned "A" and fail assigned "F".</p>
<p>Grading is based on a syllabus attestation, due on the second Wednesday of classes, and on demonstrations. Three demonstrations are required, and each has its own assignment within Canvas.</p>
<p>Due dates progress throughout the semester:</p>
<ul>
<li><a title="Syllabus Affirmation" href="" data-course-type="assignments" data-published="true">Syllabus Affirmation</a> is due by the 2nd Wednesday.</li>
<li><a title="Demonstration #1" href="" data-course-type="assignments" data-published="true">Demonstration #1</a> is due by the 6th Friday.</li>
<li><a title="Demonstration #2" href="" data-course-type="assignments" data-published="true">Demonstration #2</a> is due by the 10th Friday.</li>
<li><a title="Demonstration #3" href="" data-course-type="assignments" data-published="true">Demonstration #3</a> is due by the last Friday.</li>
</ul>
<p>Because office hours are open to potentially hundreds of researchers outside the scope of this course, <strong>only one session can be presented per student per office hours visit.</strong> <strong><em>Please plan accordingly.</em></strong></p>
<p>If for any reason you are not able to adhere to the above requirements, please contact us as soon as you know so we can make plans to accommodate you. Remember, we want you to be successful!</p>
<p>&nbsp;</p>
<h3 id="scheduling">Scheduling, Attendance &amp; Office Hours:</h3>
<p>Our course may differ from the typical university course experience. We do not host regularly scheduled course meetings. Instead, we offer twice-weekly office hours. The office hours serve two purposes for this course.</p>
<ol style="list-style-type: decimal;">
<li>Each student must make three office hours visits for the three demonstrations.</li>
<li>Students are encouraged to attend office hours if they have questions that are best answered in a virtual meeting. Past examples include:</li>
</ol>
<ul>
<li style="list-style-type: none;">
<ul style="list-style-type: disc;">
<li>Is my topic suitable for this course?</li>
<li>Where can I find more resources on topics?</li>
<li>Can you preview my demonstration material?</li>
<li>Am I on the right track?</li>
</ul>
</li>
</ul>
<p>Office Hours are held Mondays and Thursdays from 10 AM to noon via Zoom. Meeting links are available at our documentation (<a href="https://docs.rc.uab.edu/#how-to-contact-us" target="_blank" rel="noopener">https://docs.rc.uab.edu/#how-to-contact-us</a>).</p>
<p>&nbsp;</p>
<h3 id="resources">Course Resources:</h3>
<p>For students who are just entering the data science space, please consider trying some of Kaggle's micro-courses on data analysis, visualization and machine learning: <a class="inline_disabled" href="https://www.kaggle.com/learn" target="_blank" rel="noopener">https://www.kaggle.com/learn</a>.</p>
<p>For students who want to develop skills to facilitate data science, see the Software Carpentry's list of lessons: <a class="inline_disabled" href="https://software-carpentry.org/lessons/" target="_blank" rel="noopener">https://software-carpentry.org/lessons/</a>. These lessons include the Unix shell, Git version control and programming skills in Python and R.</p>
<p>For students who want to develop data literacy skills in the context of specific fields, see the Data Carpentry's list of lessons: <a class="inline_disabled" href="https://datacarpentry.org/lessons/" target="_blank" rel="noopener">https://datacarpentry.org/lessons/</a>. One of the included fields is genomics, which may be of particular interest to many UAB students.</p>
<p>For students interested in learning more about any of the above with a focus on scaling with high-performance computing, we maintain a YouTube channel with some Data Science Club Material to get you started using Cheaha: <a class="external" href="https://www.youtube.com/channel/UCZoOS2e699Ge0DND1oy1BJQ" target="_blank" rel="noopener"><span>https://www.youtube.com/channel/UCZoOS2e699Ge0DND1oy1BJQ</span></a>.</p>
<p>Here is a list of free data science resources and starting points: <a class="inline_disabled" title="Link" href="https://www.datapen.io/" target="_blank" rel="noopener">https://www.datapen.io/</a>. The following link narrows those resources down to just courses <a class="inline_disabled" title="Link" href="https://www.datapen.io/resources/free-course-resources" target="_blank" rel="noopener">https://www.datapen.io/resources/free-course-resources</a>.</p>
<p>Feel free to seek out and use other sources! If you do so, please inform us of those sources so we can curate our list and better serve future students.</p>
<p>&nbsp;</p>
<h3>Frequently Asked Questions:</h3>
<h4>I'm completely new to data science, what are some good starting points?</h4>
<ul>
<li>To get started with general data science tools and techniques, try Kaggle Learn: <a href="https://www.kaggle.com/learn" target="_blank" rel="noopener">https://www.kaggle.com/learn</a></li>
<li>Check out the Data Carpentries Lessons: <a href="https://datacarpentry.org/lessons/" target="_blank" rel="noopener">https://datacarpentry.org/lessons/</a></li>
<li>For starting bioinformatics, also try Rosalind.info: <a href="https://rosalind.info/problems/locations/" target="_blank" rel="noopener">https://rosalind.info/problems/locations/</a></li>
</ul>
<h4>What tools are available to make it easier to manage my projects?</h4>
<ul>
<li>We suggest using Git! Learn more at: <a href="https://swcarpentry.github.io/git-novice/" target="_blank" rel="noopener">https://swcarpentry.github.io/git-novice/</a></li>
</ul>
<h4>Am I allowed to use my own research projects for this course?</h4>
<ul>
<li>Yes, and we encourage applying new tools and techniques! Be mindful that we can't accept any work for research protected by IRB or using PHI/HIPAA data. Be sure to get your supervisor's approval first.</li>
</ul>
<p>&nbsp;</p>
<h3 id="support">Technical Support:</h3>
<p>Cheaha Documentation: <a class="external" href="https://docs.rc.uab.edu" target="_blank" rel="noopener">https://docs.rc.uab.edu</a>.</p>
<p>Cheaha Web Portal: <a class="external" href="https://rc.uab.edu" target="_blank" rel="noopener">https://rc.uab.edu</a>.</p>
<p>If you need software installed, or something just doesn't work like you expect, please email us at <a href="mailto:support@listserv.uab.edu" target="_blank" rel="noopener">support@listserv.uab.edu</a>. When asking for help, consider including all relevant details about your goal, what you tried, what you expected to happen, what actually happened, steps needed to reproduce the issue, and any error messages. If the error messages are longer than about 10 lines, copy-paste them into a text document and attach that to the email instead. Screenshots are also helpful. See our documentation on support (<a href="https://docs.rc.uab.edu/help/support" target="_blank" rel="noopener">https://docs.rc.uab.edu/help/support</a>) for more information.</p>
<p>&nbsp;</p>
<h3>Title IX Statement:</h3>
<p>In accordance with Title IX, the University of Alabama at Birmingham does not discriminate on the basis of gender in any of its programs or services. The University is committed to providing an environment free from discrimination based on gender and expects individuals who live, work, teach, and study within this community to contribute positively to the environment and to refrain from behaviors that threaten the freedom or respect that every member of our community deserves. For more information about Title IX, policy, reporting, protections, resources and supports, please visit the <a class="inline_disabled" href="http://www.uab.edu/titleix" target="_blank" rel="noopener">UAB Title IX webpage</a> for UAB&rsquo;s Title IX Sex Discrimination, Sexual Harassment, and Sexual Violence Policy; UAB&rsquo;s Equal Opportunity and Discriminatory Harassment Policy; and the Duty to Report and Non-Retaliation Policy.</p>
<p>&nbsp;</p>
<h3 id="dss">Disability Support Services (DSS) Statement<strong>:<br /></strong></h3>
<p>UAB is committed to providing an accessible learning experience for all students. If you are a student with a disability that qualifies under the Americans with Disabilities Act (ADA) and/or Section 504 of the Rehabilitation Act, and you require accommodations, please contact Disability Support Services for information on accommodations, registration, and procedures. Requests for reasonable accommodations involve an interactive process and consist of a collaborative effort among the student, DSS, faculty and staff. If you are registered with Disability Support Services, please contact me to discuss accommodations that may be necessary in this course. If you have a disability but have not contacted Disability Support Services, please call (205) 934-4205 or visit the <a class="inline_disabled" href="http://www.uab.edu/dss" target="_blank" rel="noopener">DSS website</a>.</p>
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<p>Hello everyone and welcome to Data Science Journal Club (DSJC)!</p>
<p>Please take a few minutes to read over the <a title="Syllabus" href="" data-course-type="navigation">syllabus</a> as it is the central repository for information about this course. There is a required, single-question, <a title="Syllabus Affirmation" href="" data-course-type="assignments" data-published="true">Syllabus Affirmation</a> quiz due the Wednesday of next week.</p>
<p>If you are new to the course, welcome! We hope you have an enlightening experience. We are happy to answer questions and provide guidance, please feel free to reach out with questions, and please read the syllabus for more detailed information about expectations.</p>
<p>If you are returning, welcome back! The syllabus may have information that is new and useful to you, we recommend reviewing it.</p>
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