Metagenomic analyses aim to explore the genomic diversity of
+ communities in specific habitats by processing their DNA sequencing
+ data. This analysis is achieved with specialized bioinformatics tools,
+ which often require previous coding experience. Furthermore, beginners
+ can struggle to build a pipeline from raw data to valuable biological
+ insights.
+
Bioinformatic tools are now essential to our understanding of
+ biological systems. Open lessons for general-purpose coding languages
+ and specialized topics such as genomics, ecology, and even
+ metagenomics are already available
+ (
The curriculum is comprised of four lessons (Fig 1). It assumes no
+ previous programming experience but expects that students understand
+ basic concepts of molecular biology and microbiology. The first two
+ lessons, introductions to project planning and organization and
+ programming in Bash respectively, are adapted from equivalent lessons
+ in the Data Carpentry Genomics curriculum
+ (
Fig 1.
Fig 1. The four lessons in the curriculum for a metagenomics + workshop.
+Project organization and management for metagenomics - Plan, + structure, organize, and document metagenomics data, metadata, and + bioinformatics workflow. - Access public data on the NCBI sequence + read archive (SRA) database.
+Introduction to the command-line for metagenomics - Identify the + benefits of the command line. - Navigate the file system, create, + copy, move, and remove files and directories. - Work with files. - + Combine commands and automate repetitive tasks. - Make an organized + file structure for a bioinformatics project.
+Introduction to R for metagenomics - Familiarize with RStudio and R + functionality. - Distinguish the different data types. - Create and + manipulate data frames. - Use and find help in R libraries.
+Data processing and visualization for metagenomics - Explain the + structure and contents of the data and metadata used in these lessons. + - Assess the quality of sequencing data. - Trim and filter sequences + based on their quality. - Perform a metagenomic assembly. - Obtain + Metagenome-Assembled Genomes and check their quality. - Assign and + visualize a taxonomy of reads and contigs. - Explore the diversity in + a sample and calculate diversity estimates. - Discover more resources + for metagenomics projects.
+The workshop includes 16 hours of content with live coding, + formative assessment practice, and other supportive elements. During + the development of the lessons, we considered three axes of teaching: + cloud setup, standardized episodes, and teaching strategies.
+-
+
Cloud setup: We set up remote machines to standardize the + learning environment and teaching experience. This setup lowers + entry barriers for students without experience in technical + installations and provides enough computing power regardless of + individual configuration. Students only need a computer with + internet access and a terminal program installed. We also enlist + the instructions for setting up the remote machines and an + alternative installation guide to be used by people who prefer to + follow the lessons on a different computer.
+Standardized episodes: Following The Carpentries instructional
+ design, lessons consist of multiple short
+
Teaching strategies
+-
+
Live coding: Programming simultaneously with students gives + a practical coding experience with examples of mistakes + arising and being solved.
+Exercises and discussion in small groups: Allows learners + to solve problems with peers and incentivizes participation + while applying what they learn to strengthen new knowledge and + skills. Regular breaks for exercises provide learners and + instructors with feedback about progress toward the learning + objectives.
+Content review: At the end and beginning of each session, + we ask learners to revisit, list, and explain the content + taught in past lessons. We use a collaborative document where + simultaneous written and spoken review helps to reaffirm the + content.
+Our teaching team includes undergraduate and graduate students, + postdocs, and professors, each with different perspectives that enrich + the discussion of the lesson. We found it adequate to have two + instructors for the online workshops, plus one helper for every five + students. We are pleased to have recruited new helpers from the + attendees of previous workshops, enlarging and further enriching our + teaching community. To promote an interactive learning experience, we + use a collaborative live document and small groups to do exercises and + discussions. In this way, there are fewer barriers to student’s + participation, and they gain practical experience of the different + solutions bioinformatic problems can have. We include bonus exercises + around the lessons that are not meant to be solved by all the learners + but are an opportunity for advanced participants to tackle more + challenging tasks. They help to leverage the background and learning + speed of the learners and provide opportunities to practice and + reinforce the content learned. Another strength of our workshop + structure is introducing programming languages followed by a practical + example of their usage, so the metagenomic analysis grows while the + coding skills learned become meaningful. The lessons are helpful even + if the student’s primary goal is to learn coding rather than + metagenomics. We ask the attendees to fill out surveys before, during, + and after the workshops to adapt our teaching strategies to the + current and future learning groups. With the results of these surveys, + we have been able to improve the curriculum’s content, explanations, + and exercises.
+The idea to create a lesson comprising all of the steps required to + process and analyze metagenomics data arose when one of the + development team wanted to learn how to understand metagenomics data + but found it overwhelming even to decide where to start. As someone + who already used and knew the advantages of the resources offered by + The Carpentries, she recognized the absence of a curriculum about + metagenomics on this platform. When she learned of The Carpentries + Incubator, she reached out to a fellow student who had experience on + the subject and started building the episodes. Other students in the + same institute, who were also working on metagenomics, started + contributing to the pipelines they were learning. Further team members + were recruited as helpers after attending a workshop and later began + collaborating to develop the episodes.
+Karina Enríquez Guillén and Rafael Pérez Estrada for testing and + improving the lesson content. Diana Oaxaca, Alejandro Pereira Santana, + Angélica Ruiz, Brian Bwanya, Ahmed Moustafa and Israel Pichardo, for + enriching content and teaching strategy. Angélica Cibrián-Jaramillo, + Francisco Barona-Gómez, and Harumi Shimada enabled and promoted the + delivery of these lessons among their communities. Developers of Data + Carpentry Genomics for their work and ideas. Toby Hodges and Erin + Becker for their technical support during the development and delivery + of the lessons. Students for their feedback and enthusiasm. We thank + UNAM for funding in proyecto PAPIME “Desarrollo de material didáctico + de Bioinformática con énfasis en metagenómica para las modalidades + presencial y virtual”
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