Bianca Peterson on The Carpentries

Feedback: Remote Teaching of Genomics Data Carpentry Curriculum

Fri, 24 Jan 2020 00:00:00 +0000

The People

A Genomics Data Carpentry Workshop was organised by and taught at the International Centre of Insect Physiology and Ecology ICIPE in Nairobi, Kenya. Daniel Ouso was the on-site instructor, while Bianca Peterson taught remotely from South Africa. We also had amazing local helpers: Caleb Kibet, Careen Natoire, and Gilbert Kibet

We had one completed BSc., three continuing Ph.D.s, one completed M.Sc., and the rest of the participants were continuing M.Sc.s. The main fields of study of most participants were genetics, genomics and bioinformatics. Participants were mostly Windows users and a little under 40% had zero programming experience. We had more females than males attending the workshop.

With Thanks from Carpentries Instructors in Africa

Thu, 12 Dec 2019 00:00:00 +0000

The African Instructors Community is made up of individuals who volunteer their time to teach foundational coding and data science skills to researchers on the continent. Ending 2019 on a positive note, not only was there a growth in the number of trained instructors, an increase in African countries joining The Carpentries community, but a Regional Consultant for Southern Africa has also been appointed to support the team of volunteer instructors across the continent.

CarpentryCon 2020: Tips for Submitting a Session Proposal

Thu, 07 Nov 2019 00:00:00 +0000

CarpentryCon is one of the most awaited events of The Carpentries for community building and networking. The theme for CarpentryCon 2020 is “Growing inclusive, computational communities and leaders.” This three-day event brings together new and experienced community members to share knowledge, network, develop new skills, and exchange strategies for building local communities of practice. The conference will be at the University of Wisconsin - Madison, USA from 29 June to 1 July, 2020. Come and help develop the next generation of leaders through practical skill-ups, networking, workshops, and breakout sessions.

Announcing CarpentryCon 2020 Dates, Location and Theme

Wed, 31 Jul 2019 00:00:00 +0000

Thanks to the efforts of the whole Carpentries Community, we received a number of great suggestions/bids for CarpentryCon2020’s theme and venue. Many thanks to those who took time to suggest a theme or submit a venue bid.

Read more about the theme and venue below and bookmark the CarpentryCon2020 website for additional updates.

CarpentryCon 2020: Meet Up in Madison, Wisconsin, USA!

We are excited to announce that CarpentryCon2020 will be held on June 29 - July 1st, 2020 at the University of Wisconsin - Madison (Madison, Wisconsin, United States).

Tips and Tricks for Teaching R

Fri, 17 May 2019 00:00:00 +0000

Following a few Data Carpentry workshops, we (a.k.a. Bianca and Katrin) shared some of the strategies we employ to enhance participants’ R learning experience in a Community Discussion with other Carpentries Instructors from Africa. In this post, we will expound on some of these strategies and welcome you to try them in the workshops you facilitate, and share your outcomes with the broader Carpentries community.

Pen-on-paper exercise

In the R episodes on Data Manipulation and on Visualisation, code and challenges become quite complex and may contain new concepts of coding as well as of data analysis for novices. Individual code blocks can easily run over several lines when using pipes (%>%) or when building plots with ggplot, thus increasing cognitive load for learners. To enhance understanding of the concepts behind the R commands and also to give participants a break from sitting in front of the computer, we included group exercises with pen and paper. We divided participants into groups of four to five and gave each group a blank sheet of paper (it works particularly nice with big sheets stuck to a wall so the groups can stand around it). We then wrote a challenge on the Workshop Etherpad/whiteboard and asked the groups to discuss and write down the steps (not necessarily the commands) they would need to subset their data accordingly.

16S Metagenomics Workshop based on Data Carpentry: successes and challenges

Mon, 20 Nov 2017 00:00:00 +0000

This post originally appeared on the Data Carpentry website

We ran a 16S metagenomics workshop based on Data Carpentry materials at the North-West University, South Africa, from 24-27 October. A combination of lessons from Data Carpentry, as well as specific workflows for 16S data analysis, were used. We modified most of the lessons according to our main (critical) lesson’s dataset that we were using for 16S analysis. The following topics were covered: spreadsheet organization, shell, 16S analyses on HPC (using Shi7, NINJA and QIIME), R genomics and specific plots of 16S data in R. We extended the workshop to three full days to fit in all the lessons and decided on an additional half-day where attendees would have the opportunity to work on their own data. Twenty-three participants attended the whole workshop.

My Favourite Tool - R

Mon, 06 Nov 2017 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

R can do anything - from making presentations, analyzing and plotting data to version control (Git).

I use it for absolutely everything! It’s not difficult to use and it’s free!

– Bianca Peterson, Temporary lecturer (Microbiology) & Project Coordinator (IT), South Africa

Have you got a favourite tool you would like to tell us about? Please use this form to add a bit of detail and we will do the rest. You can read the background to these posts here, or see what other tools people have written about.

Building Genomics Data Analysis Capacity at NWU

Wed, 07 Dec 2016 00:00:00 +0000

This post originally appeared on the Data Carpentry website

The North-West University in South Africa boasts two next generation sequencing (NGS) platforms and additionally receive terabytes of NGS data annually from local and international service providers. Research projects with NGS components exist in the areas of Microbiology, Zoology, Botany, Nutrition, Agriculture, and more.

The three biggest challenges experienced by researchers and postgraduate students in terms of data analysis are as follow:

many of the students entering NGS projects have limited prior exposure to molecular techniques such as Sanger sequencing and PCR, and genetics concepts;
there is limited access to bioinformatics support and training (although there is lots of access to short interventions like 1- or 2-day workshops with no sustained follow-up);
and they are not aware of the range of research compute infrastructures which are available to them.

In September 2016, the NWU eResearch Initiative helped to establish a Genomics Hacky Hour (GHH) Study Group to support postgraduate students and researchers using NGS technologies. The original intention of the GHH was to bring researchers together to work on their current projects. However, limited shared NGS vocabulary hampered constructive communication amongst researchers and it was decided that specific topics would be discussed during the first few sessions, lead by a study group leader.

1 - 30 June, 2016: Efficacy and Usefulness, Minutes, Discussions, Onboarding Documents, Teaching Undergraduates, and Library Carpentry Material

Thu, 30 Jun 2016 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

##Highlights

Have you previously attended a Software Carpentry workshop? Get involved with the follow-up study on “The Efficacy and Usefulness of Software Carpentry Training” by completing a survey. Feedback on your experience will be greatly appreciated!
Minutes of the Steering Committee Meeting is available - suggestions to modify the workflow of the minutes are welcome!

##Discussions

Please add your comments to the topics in ongoing discussions.
There is a discussion on the mailing list about “onboarding” documents for laboratories or small research groups. Also see Lab Carpentry.
Mexican/Spanish speaking instructors are needed for a Software Carpentry workshop later in the year. Please let us know if you’re interested to teach.
Read about approaches and experiences on teaching python to undergraduate geoscientists.

##Other

9 - 31 May, 2016: The First Bimonthly Report, Instructor Data Analysis, R Instructor Training, Measuring the Right Stuff, RSE Conference, and a Bug Barbeque

Tue, 31 May 2016 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

##Highlights

The 2016 Steering Committee’s first bimonthly report provides an overview on happenings in the community in the past two months. The joint partnership agreement with Data Carpentry is now available, together with a written version of the instructor training model, a call for subcommittees and task forces, and an official space on Facebook. Make sure to read the Code of Conduct in support of our welcoming, friendly, and diverse community.

##Instructor training

24 April - 4 May, 2016: Subcommittees and Task Forces, Partnerships, Instructor Training, A Vacancy, Lab Meeting, Bug Barbeque, Discuss, and New Videos and a Book

Mon, 09 May 2016 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

Highlights

The 2016 Steering Committee invites you to help organize and develop resources and activities to support our community members by proposing new initiatives in the form of subcommittees and task forces. Full instructions on the proposal process can be found here. The Steering Committee will gladly help! Also check out the subcommittee listing for information on existing and past subcommittees.
Joint partnerships are now offered by Data Carpentry and Software Carpentry! Read the partnership information on how to become a partner and get in touch.

Vacancy

Data Carpentry is hiring a Deputy Director of Assessment. Visit the Data Carpentry jobs page for a full job description and application procedure.

Events

Tune in to the Software Carpentry Lab Meeting on May 10th to discuss what’s new and upcoming in the community. Check out the Lab Meeting Etherpad for the schedule and connection details.
Join the worldwide Software Carpentry Bug Barbeque on June 13 to help fix bugs in Version 5.4 of Software Carpentry lessons before publication. All contributors will receive credit for your hard work with a citable object.

Conversations

A recent conversation on the discuss mailing list prompted the creation of two new issues open for discussion in GitHub:
- How should we deal with high-volume discussions on the mailing list?
- Is the Code of Conduct saying what the community want/need it to say and how should it be enforced?

Videos and Books

Greg Wilson published a video of “things not to do while teaching”. The material is great to use during instructor training to demonstrate to instructor trainees what we’re trying to avoid when teaching and is based on suggestions made in this discussion on GitHub.
Support Data Carpentry by buying the book How to Be a Modern Scientist written by Jeff Leek. The book includes guides for reviewing papers, reading papers, career planning, and giving talks.
Iñigo Aldazabal Mensa (CSIC-UPV/EHU) provided a video of him explaining Software Carpentry in great detail at the 2016 HPC Knowledge Portal Conference - Software Carpentry: teaching computing skills to researchers.

Other

Did you recently participate in a Software Carpentry workshop and had questions that weren’t answered by the lessons? Do you teach workshops and hear questions from participants that can’t be addressed by the existing materials? Please add these questions to this post.
What have we learned from our lesson discussion sessions so far? We welcome all new instructors to provide feedback about their experience of the sessions by commenting on the post.
Aleksandra Pawlik recently blogged about her experience when she visited South Africa for the first face-to-face Software and Data Carpentry Instructor Training in Africa.
Planning on running a Software Carpentry workshop with R? Read how three sticky notes and chocolates helped participants in the Sotware Carpentry workshop at Griffith University.
Staff members from iDigBio gave their perspective on attending a Software Carpentry workshop. They encourage all researchers who’d like to work with the iDigBio datasets to particpipate in a workshop near them or request one at their own institution.
16 workshops were run over the past 16 days. For more information about past workshops, please visit our website.
Upcoming Workhshops

4 - 18 March, 2016: Instructor Trainee Mentoring, Debriefing vs Lesson Sessions, Version Control, Big Data in Biology Summer School, New Lessons

Fri, 18 Mar 2016 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

##Instructor Training

How can we help instructor trainees complete their training? Belinda Weaver is working hard to support new instructors in Australia. Do you have any other ideas?
Several opportunities are now available for new and experienced instructors to join the conversations about workshops. Should we be combining various sessions to better integrate new and old instructors and give more options for participation?
You can also read about the abovementioned discussions in the latest summary of instructor debriefing rounds 4 and 5.

##Conversations