| layout | venue | address | country | language | latitude | longitude | humandate | humantime | startdate | enddate | instructor | helper | collaborative_notes | eventbrite | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
workshop |
Duke University |
Wed, Aug 21: MSRB III Room 1125<br> Thurs-Fri, Aug 22-23: GSRB1 Room 4002 (Front sign says <q>Snyderman Genome Science Research Building</q>) |
us |
en |
36 |
-78 |
Aug 21-23, 2024 |
9:00am - 3:30pm |
2024-08-21 |
2024-08-23 |
|
|
{% comment %} See instructions in the comments below for how to edit specific sections of this workshop template. {% endcomment %}
{% comment %} HEADER
Edit the values in the block above to be appropriate for your workshop. If the value is not 'true', 'false', 'null', or a number, please use double quotation marks around the value, unless specified otherwise. And run 'make workshop-check' before committing to make sure that changes are good. {% endcomment %}
{% comment %} 8< ============= For a workshop delete from here ============= For a workshop please delete the following block until the next dashed-line {% endcomment %}
{% comment %} 8< ============================= until here ================== {% endcomment %}
{% comment %} Check DC curriculum {% endcomment %}
{% if site.carpentry == "dc" %} {% unless site.curriculum == "dc-astronomy" or site.curriculum == "dc-ecology" or site.curriculum == "dc-genomics" or site.curriculum == "dc-geospatial" or site.curriculum == "dc-image" or site.curriculum == "dc-socsci" %}
_config.yml file (current value in _config.yml: "{{ site.curriculum }}", possible values: dc-image, dc-astronomy, dc-ecology, dc-genomics, dc-socsci, or dc-geospatial). After editing this file, you need to run make serve again to see the changes reflected.
{% comment %} Check SWC curriculum {% endcomment %}
{% if site.carpentry == "swc" %} {% unless site.curriculum == "swc-inflammation" or site.curriculum == "swc-gapminder" %}
_config.yml file (current value in _config.yml: "{{ site.curriculum }}", possible values: swc-inflammation, or swc-gapminder). After editing this file, you need to run make serve again to see the changes reflected.
{% comment %} EVENTBRITE
This block includes the Eventbrite registration widget if 'eventbrite' has been set in the header. You can delete it if you are not using Eventbrite, or leave it in, since it will not be displayed if the 'eventbrite' field in the header is not set. {% endcomment %} {% if page.eventbrite %} Some adblockers block the registration window. If you do not see the registration box below, please check your adblocker settings.
<iframe src="https://www.eventbrite.com/tickets-external?eid={{page.eventbrite}}&ref=etckt" frameborder="0" width="100%" height="280px" scrolling="auto"> </iframe> {% endif %}{% comment %} INTRODUCTION
Edit the general explanatory paragraph below if you want to change the pitch. {% endcomment %}
Welcome to the UPGG Computational Bootcamp!!
As genetic techonology advances and the demand for analyzing larger data grows, it is pivotal to develop some background in computational skills. You need basic command line knowledge to operate powerful bioinformatic software and tools, as well as some coding to make both impactful and aesthetically appealing visualization of your research. In this bootcamp, we will touch on basic command lines in Unix and how to manipulate and visualize data in R. Since the best way to learn programing is to try it yourself, we focus on live-coding and have prepared a group project on the last day in which you can explore and utilize your skills freely! Lastly, this bootcamp is mostly student-run and is instructed by peer instructors -- PhD students in UPGG. All of us were, at one point, sitting where you are!
This course website was built in courtesy of The Carpentries project.{% if site.pilot %} This is a pilot workshop, testing out a lesson that is still under development. The lesson authors would appreciate any feedback you can give them about the lesson content and suggestions for how it could be further improved. {% endif %}
{% comment %} AUDIENCE
Explain who your audience is. (In particular, tell readers if the workshop is only open to people from a particular institution. {% endcomment %} {% if site.carpentry == "swc" %} {% include swc/who.html %} {% elsif site.carpentry == "dc" %} {% include dc/who.html %} {% elsif site.carpentry == "lc" %} {% include lc/who.html %} {% endif %}
{% comment %} LOCATION
This block displays the address and links to maps showing directions if the latitude and longitude of the workshop have been set. You can use https://www.latlong.net/ to find the lat/long of an address. {% endcomment %} {% assign begin_address = page.address | slice: 0, 4 | downcase %} {% if page.address == "online" %} {% assign online = "true_private" %} {% elsif begin_address contains "http" %} {% assign online = "true_public" %} {% else %} {% assign online = "false" %} {% endif %} {% if page.latitude and page.longitude and online == "false" %}
Where: {{page.address}}. Get directions to GSRB1 and MSRB III.
{% elsif online == "true_public" %}Where: online at {{page.address}}. If you need a password or other information to access the training, the instructor will pass it on to you before the workshop.
{% elsif online == "true_private" %}Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.
{% endif %}{% comment %} DATE
This block displays the date and links to Google Calendar. {% endcomment %} {% if page.humandate %}
When: {{page.humandate}}. {% include workshop_calendar.html %}
{% endif %}{% comment %} SPECIAL REQUIREMENTS
Modify the block below if there are any special requirements. {% endcomment %}
Requirements: {% if online == "false" %} Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. {% else %} Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. {% endif %} They should have a few specific software packages installed (listed below).
{% comment %} ACCESSIBILITY
Modify the block below if there are any barriers to accessibility or special instructions. {% endcomment %}
Accessibility: {% if online == "false" %} We are committed to making this bootcamp accessible to everybody.
- The rooms are wheelchair / scooter accessible.
- Accessible restrooms are available.
Please get in touch (using contact details below) if we can help making learning easier for you, and we will attempt to provide them.
{% comment %} CONTACT EMAIL ADDRESS
Display the contact email address set in the configuration file. {% endcomment %}
Contact: Please email {% if page.email %} {% for email in page.email %} {% if forloop.last and page.email.size > 1 %} or {% else %} {% unless forloop.first %} , {% endunless %} {% endif %} {{email}} {% endfor %} {% else %} to-be-announced {% endif %} for more information.
{% comment %} WHO CAN ATTEND?
If you would like to specify who can attend the workshop, you can use the section below.
Move the 'endcomment' tag above the beginning of the following
tag to make this section visible.
Edit the text to match who can attend the workshop. For instance:
- This workshop is open to affiliates to ABC university.
- This workshop is open to the public.
- If you are interested in attending this workshop, contact [email protected] for more information
Who can attend?: This workshop is open to ....
{% endcomment %}{% comment %} Collaborative Notes
If you want to use an Etherpad, go to
https://pad.carpentries.org/YYYY-MM-DD-site
where 'YYYY-MM-DD-site' is the identifier for your workshop, e.g., '2015-06-10-esu'.
Note we also have a CodiMD (the open-source version of HackMD) available at https://codimd.carpentries.org {% endcomment %} {% if page.collaborative_notes %}
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
{% endif %}
{% comment %} SURVEYS - DO NOT EDIT SURVEY LINKS {% endcomment %}
Please be sure to complete the survey after each lesson and the overall bootcamp.
{% comment %} SCHEDULE
Show the workshop's schedule.
Small changes to the schedule can be made by modifying the
schedule.html found in the _includes folder for your
workshop type (swc, lc, or dc). Edit the items and
times in the table to match your plans. You may also want to
change 'Day 1' and 'Day 2' to be actual dates or days of the
week.
For larger changes, a blank template for a 4-day workshop
(useful for online teaching for instance) can be found in
_includes/custom-schedule.html. Add the times, and what
you will be teaching to this file. You may also want to add
rows to the table if you wish to break down the schedule
further. To use this custom schedule here, replace the block
of code below the Schedule <h2> header below with
{% include custom-schedule.html %}.
{% endcomment %}
{% if site.carpentry == "swc" %} {% include swc/schedule.html %} {% elsif site.carpentry == "dc" %} {% include dc/schedule.html %} {% elsif site.carpentry == "lc" %} {% include lc/schedule.html %} {% elsif site.carpentry == "incubator" %} This workshop is teaching a lesson in The Carpentries Incubator. Please check [the lesson homepage]({{ site.incubator_lesson_site }}) for a list of lesson sections and estimated timings. {% endif %}
{% comment %} Edit/replace the text above if you want to include a schedule table. See the contents of the _includes/custom-schedule.html file for an example of how one of these schedule tables is constructed. {% endcomment %}
{% if site.pilot %} The lesson taught in this workshop is being piloted and a precise schedule is yet to be established. The workshop will include regular breaks. Please contact the workshop organisers if you would like more information about the planned schedule. {% endif %}
{% comment %} SYLLABUS
Show what topics will be covered.
- If your workshop is R rather than Python, remove the comment around that section and put a comment around the Python section.
- Some workshops will delete SQL.
- Please make sure the list of topics is synchronized with what you intend to teach.
- You may need to move the div's with class="col-md-6" around inside the div's with class="row" to balance the multi-column layout.
This is one of the places where people frequently make mistakes, so please preview your site before committing, and make sure to run 'tools/check' as well. {% endcomment %}
{% if site.carpentry == "swc" %} {% include swc/syllabus.html %} {% elsif site.carpentry == "dc" %} {% include dc/syllabus.html %} {% elsif site.carpentry == "lc" %} {% include lc/syllabus.html %} {% endif %}
{% comment %} SETUP
Delete irrelevant sections from the setup instructions. Each section is inside a 'div' without any classes to make the beginning and end easier to find.
This is the other place where people frequently make mistakes, so please preview your site before committing, and make sure to run 'tools/check' as well. {% endcomment %}
To participate in a {% if site.carpentry == "swc" %} Software Carpentry {% elsif site.carpentry == "dc" %} Data Carpentry {% elsif site.carpentry == "lc" %} Library Carpentry {% endif %} workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.
{% comment %} For online workshops, the section below provides:
- installation instructions for the Zoom client
- recommendations for setting up Learners' workspace so they can follow along the instructions and the videoconferencing
If you do not use Zoom for your online workshop, edit the file
_includes/install_instructions/videoconferencing.html
to include the relevant installation instructions.
{% endcomment %}
{% if online != "false" %}
{% include install_instructions/videoconferencing.html %}
{% endif %}
{% comment %} These are the installation instructions for the tools used during the workshop. {% endcomment %}
{% if site.carpentry == "swc" %} {% include swc/setup.html %} {% elsif site.carpentry == "dc" %} {% include dc/setup.html %} {% elsif site.carpentry == "lc" %} {% include lc/setup.html %} {% elsif site.carpentry == "incubator" %} Please check the "Setup" page of [the lesson site]({{ site.incubator_lesson_site }}) for instructions to follow to obtain the software and data you will need to follow the lesson. {% endif %}