This is a module of the CIEE Living Data Project. Access to this Canvas site and associated materials is restricted to registered participants. To find out more about the Living Data Project, visit [https://www.ciee-icee.ca/ldp.html Links to an external site.](https://www.ciee-icee.ca/ldp.html). {alt="welcome_datamanagement.jpg"} ### **Teaching team** #### Lead instructor(s): - Prof. Rachel Germain, University of British Columbia---Vancouver ([rgermain\@zoology.ubc.ca](mailto:rgermain@zoology.ubc.ca)) - Sally Taylor, Head Librarian, Woodward Library, University of British Columbia---Vancouver ([sally.taylor\@ubc.ca](mailto:sally.taylor@ubc.ca)) - Prof. Raymond Ng, University of British Columbia---Vancouver ([rng\@cs.ubc.ca](mailto:rng@cs.ubc.ca)) #### LDP postdocs: - Dr. Gracielle Higino, University of British Columbia---Vancouver ([higino\@zoology.ubc.ca](mailto:higino@zoology.ubc.ca)) - Dr. Mike Lavender, University of Regina ([thomas.lavender\@uregina.ca](mailto:thomas.lavender@uregina.ca)) - Dr. Sam Straus, McGill University and Université de Montréal ([samantha.straus\@mcgill.ca](mailto:samantha.straus@mcgill.ca)) #### Teaching assistants: - Liam Johnson, University of British Columbia---Okanagan ([liamgwj\@mail.ubc.ca](mailto:liamgwj@mail.ubc.ca))    ### **Course description** This course will develop best practices in data management in ecology and evolution research. We will use a combination of instruction, in-class activities and projects to guide students through all parts of the research data lifecycle, starting with the collection and storage of data, progressing through the organizing of data (database design, \"tidy\" data principles, data versioning), the cleaning of data (quality assessment, geospatial and taxonomic data standards), and ending with the sharing of data (metadata and documentation, and archiving and accessing data in digital repositories following the new FAIR principles). Each student will work progressively through the course on an individual data management plan for the data they will collect - or have already collected - for one of their research projects. As well, students will work in small groups on preparing an existing biological dataset for archiving using R scripts. This course, one of the first such courses in Canada specifically geared to ecology and evolution, will give students the tools for managing their own research data as well as rescuing previously collected data.   ### **Meeting times** 06 September to 29 September 2022 Tue/Thu 10:00 am - 11:30 am PDT\ Tue/Thu 11:00 am - 12:30 pm CST + MDT\ Tue/Thu 1:00 pm - 2:30 pm EDT **Week 1**: Tue 06 Sep ([lesson 1](https://canvas.ubc.ca/courses/97662/modules/605223 "Lesson 1 (Tue 07 Sep 2021): "add short description here"")), Thu 08 Sep ([lesson 2](https://canvas.ubc.ca/courses/97662/modules/605224 "Lesson 2 (Thu 09 Sep 2021): "add short description here""))\ **Week 2**: Tue 13 Sep ([lesson 3](https://canvas.ubc.ca/courses/97662/modules/605225 "Lesson 3 (Tue 14 Sep 2021): "add short description here"")), Thu 15 Sep ([lesson 4](https://canvas.ubc.ca/courses/97662/modules/605226 "Lesson 4 (Thu 16 Sep 2021): "add short description here""))\ **Week 3**: Tue 20 Sep ([lesson 5](https://canvas.ubc.ca/courses/97662/modules/605227 "Lesson 5 (Tue 21 Sep 2021): "add short description here"")), Thu 22 Sep ([lesson 6](https://canvas.ubc.ca/courses/97662/modules/605228 "Lesson 6 (Thu 23 Sep 2021): "add short description here""))\ **Week 4**: Tue 27 Sep ([lesson 7](https://canvas.ubc.ca/courses/97662/modules/605229 "Lesson 7 (Tue 28 Sep 2021): "add short description here"")), Thu 29 Sep ([lesson 8](https://canvas.ubc.ca/courses/97662/pages/outline-lesson-8 "Outline - Lesson 8"))   **Zoom link** Classroom:\ [https://ubc.zoom.us/j/68865074356?pwd=S25Qb0UwaWM3bDdUZ2xXcmZOa0M2UT09Links to an external site.](https://ubc.zoom.us/j/68865074356?pwd=S25Qb0UwaWM3bDdUZ2xXcmZOa0M2UT09) Time: Sep 6, 2022 10:00 Pacific Time (US and Canada)\         Every week on Tue, Thu, until Sep 29, 2022, 8 occurrence(s)\         Sep 6, 2022 10:00\         Sep 8, 2022 10:00\         Sep 13, 2022 10:00\         Sep 15, 2022 10:00\         Sep 20, 2022 10:00\         Sep 22, 2022 10:00\         Sep 27, 2022 10:00\         Sep 29, 2022 10:00 Please download and import the following iCalendar (.ics) files to your calendar system.\ Weekly: https://ubc.zoom.us/meeting/u5wlceyoqT8pH9K_g8KcaDBQSkTPjrxl0-uL/ics?icsToken=98tyKu-gpj0vGtORsxyBR_M-Go_oZ_Twtilegvp2oxi9KCNSRiHHBel2ArhtCNSA Meeting ID: 688 6507 4356\ Passcode: 786114[Links to an external site.](https://ubc.zoom.us/j/68865074356?pwd=S25Qb0UwaWM3bDdUZ2xXcmZOa0M2UT09) One tap mobile\ +17789072071,,68865074356#,,,,,,0#,,786114#[Links to an external site.](https://ubc.zoom.us/j/68865074356?pwd=S25Qb0UwaWM3bDdUZ2xXcmZOa0M2UT09) Dial by your location\ +1 778 907 2071 (Vancouver)\ +1 647 374 4685 (Toronto)\ +1 647 375 2970 (Toronto)\ +1 647 375 2971 (Toronto)\ +1 204 272 7920 (Manitoba)\ +1 438 809 7799 (Montreal)\ +1 587 328 1099 (Alberta)\ +1 613 209 3054 (Ottawa)[Links to an external site.](https://ubc.zoom.us/j/68865074356?pwd=S25Qb0UwaWM3bDdUZ2xXcmZOa0M2UT09) Meeting ID: 688 6507 4356\ Passcode: 786114[Links to an external site.](https://ubc.zoom.us/j/68865074356?pwd=S25Qb0UwaWM3bDdUZ2xXcmZOa0M2UT09) Join from a videoconferencing system\ IP: 65.39.152.160\ Meeting ID: 688 6507 4356\ Passcode: 786114[Links to an external site.](https://ubc.zoom.us/j/68865074356?pwd=S25Qb0UwaWM3bDdUZ2xXcmZOa0M2UT09) SIP: 68865074356\@vn.zmca.us\ Passcode: 786114 [Links to an external site.](https://ubc.zoom.us/j/68865074356?pwd=S25Qb0UwaWM3bDdUZ2xXcmZOa0M2UT09) ### **Delivery format** - 8 sessions, 1.5 hours per session - Each session generally includes a lecture and hands-on component, varying in length among sessions   ### **Anticipated time commitment** In general, students in each Living Data Project module should anticipate approximately 30-45 work hours, in line with the normal expectations for one credit of coursework. This will comprise the following activities: 12 hours formal instruction in a class setting, 4 hours of individual/small group mentoring, 5 hours of preparatory reading, up to 15 hours on required assignments. Assignments are completed progressively as the course proceeds to allow instructor feedback on drafts, with a final version of major projects due within a week of course completion   ### **Pre-requisites and pre-course preparations** - Graduate-level thesis in ecology, evolutionary biology, or environmental science - In order to create a Data Management Plan (major part of course grade), you are at a stage where you have an idea of what data you are likely to collect for part of your thesis, or you have already collected data for your thesis or a previous research project. - Introductory R programming experience (i.e. base R) - Consult pre-course training resources [here](https://canvas.ubc.ca/courses/97662/pages/instructions-for-students-r-and-rstudio "Pre-course training resources") (also see Require Materials below)   ### **Required materials** - Personal computer with videoconferencing ability and reliable internet access - R and RStudio - Please see [these instructions](https://canvas.ubc.ca/courses/97662/pages/instructions-for-students-r-and-rstudio "Instructions for students: R and RStudio") for installing the latest versions R and RStudio, or checking which versions you're currently running **Note**: we focus on the use of open-source and free software and tools to maximize accessibility.   ### **Learning outcomes** - Understand and be able to implement best practices in managing research data, including the documentation, validation, structuring, storage and archiving of data. - Creation of a data management plan suitable for student's own research data - Understand the process for structuring, validating and cleaning data, including hands-on implementation in R - Conceptual understanding of relational databases: why we need them and how they work - Ability to create comprehensive and useful metadata - Familiarity with data repositories in ecology and evolution - Understand the process for rescuing and archiving previously collected data, and the need for such data rescue - This course, in combination with the Living Data Project's Synthesis Statistics course, fulfils the prerequisites for an LDP data rescue internship for students at UBC, McGill, University of Regina and Université de Montréal   ### **Assessments** - [Data Management Plan](https://canvas.ubc.ca/courses/97662/assignments/1189491 "Data Management Plan (individual assignment)") (60%; individual) --- develop a DMP for your thesis research\ Due dates: [Midpoint version](https://canvas.ubc.ca/courses/97662/assignments/1189489 "DMP Midpoint Submission") **due Friday 23 September 11:59pm PDT**; [final version](https://canvas.ubc.ca/courses/97662/assignments/1189491 "Data Management Plan (individual assignment)") **due Friday, October 7 at 11:59pm PDT** - [Data Cleaning & Standards Assignment](https://canvas.ubc.ca/courses/97662/assignments/1189490 "Data Cleaning and Standards (individual/group assignment)") (40%; individual with group input) --- write a short script to resolve a common data cleaning task\ Due date: **Friday September 16th by 11:59pm PDT**   ### **Lecture slides, readings, recordings** You can find the material for each lecture (including slides, readings and video recordings) under [**Modules**](https://canvas.ubc.ca/courses/97662/modules "Modules")(see menu at left). We realize that you may also wish to access these materials after the course ends, so we will also archive all public materials for this and associated Living Data Project courses on the Open Science Framework (OSF) component and wiki pages for the [Living Data Project Links to an external site.](https://osf.io/ych3w/)(see the course outline [here Links to an external site.](https://osf.io/sjf2g/wiki/Course%20outline/)). This archiving will occur at the end of the course (currently only the previous year's course is archived on OSF).   ### **Office hours / Getting help** #### Office hours Postdocs will host weekly open office hours where you can ask questions about course material, assignments, LDP training opportunities, career development, etc. Students are welcome to attend any office hours that work with their schedule. - **Wednesdays** \@ 1:00 pm - 2:00 pm EDT / 11:00 am - 12:00 pm CST + MDT / 10:00 am - 11:00 am PDT (Mike and Liam)\ [Join Zoom meeting Links to an external site.](https://uregina-ca.zoom.us/j/94741619853?pwd=UENFM3ZKTmNEY1pVdFNaSyt5QzFrUT09)(meeting ID: 947 4161 9853; passcode: 890794) - **Thursdays** \@ 4:00 pm - 5:00 pm EDT / 2:00 pm - 3:00 pm CST + MDT / 1:00 pm - 2:00 pm PDT (Gracielle and Sam)\ [Join Zoom meeting Links to an external site.](https://ubc.zoom.us/j/61974399606?pwd=M3p3cERMMkV2RzdpZ2g1Q0M5MDdLZz09)(meeting ID: 619 7439 9606; passcode: 986168)   #### Getting help For help with course material, students are encouraged to contact their primary mentor as follows: - **UBC-V** and **CIEE member universities\***: Gracielle Higino ([higino\@zoology.ubc.ca](mailto:higino@zoology.ubc.ca)) - **Regina** and **UBC-O**: Mike Lavender ([thomas.lavender\@uregina.ca](mailto:thomas.lavender@uregina.ca)) - **UdeM**, **McGill**, and **CSEE-affiliated students\*\***: Sam Straus ([samantha.straus\@mcgill.ca](mailto:samantha.straus@mail.mcgill.ca)) **\*** Other CIEE member universities: Carleton, Simon Fraser, Guelph, Manitoba, UQaM, Queen's, Toronto **\*\*** CSEE-affiliated students: participants from all other Canadian universities   You can email the postdocs or course instructor directly from Canvas by navigating to your [Inbox](https://canvas.ubc.ca/conversations#filter=type=inbox) (this will send an email through the address you used to create your CWL). If you cannot reach your designated mentor, please feel free to contact another instructor or teaching assistant.   ### **Code of conduct** Participation in this course and all other functions of the Living Data Project requires adherence to our [Code of Conduct](https://canvas.ubc.ca/courses/97662/pages/ldp-code-of-conduct "LDP Code of Conduct"). Please review the Code of Conduct before the beginning of the first class.   **UBC students connecting from outside Canada are directed to read [this statement](https://canvas.ubc.ca/courses/97662/pages/statement-for-review-by-international-students-at-ubc "Statement for review by international students at UBC").**   ### **Territorial acknowledgement** The Living Data Project is a collaborative effort by researchers at institutions across Canada. We collectively acknowledge that we live and work on the traditional, ancestral, treaty, and unceded territories of many Indigenous peoples, including the Coast Salish Peoples, xwməθkwəy̓əm (Musqueam), Syilx (Okanagan), nêhiyawak (Cree), anihšināpēk (Saulteaux), Dakota, Lakota, Nakoda, Attawanderon, Mississaugas, kanien\'kehà:ka (Mohawk), and Haudenosaunee, and the homeland of the Métis/Michif Nation. The LDP brings together instructors and students from many different places with distinct Indigenous traditions and colonial histories.  We encourage all participants to seek more information about the traditional territories on which they live: [https://native-land.caLinks ](https://native-land.ca/)