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Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops

Matthew R. Dillon, Evan Bolyen, Anja Adamov, Aeriel Belk, Emily Borsom, Zachary Burcham, Justine W. Debelius, Heather Deel, Alex Emmons, Mehrbod Estaki, Chloe Herman, Christopher R. Keefe (+20 others)
2021 PLoS Computational Biology  
In January of 2021, we followed this workshop with a second fully online workshop, incorporating lessons from the first.  ...  In October of 2020, in response to the Coronavirus Disease 2019 (COVID-19) pandemic, our team hosted our first fully online workshop teaching the QIIME 2 microbiome bioinformatics platform.  ...  Acknowledgments We would like to thank all participants and viewers who attended our online workshops and provided feedback on these events.  ... 
doi:10.1371/journal.pcbi.1009056 pmid:34166363 fatcat:x5zakidnjnecpdshmoykwobhrm

CFDE Training Assessment - 2020-2021

Amanda Charbonneau, Saranya Canchi, Marisa C.W. Lim, Abhijna Parigi, Jose Sanchez, Jeremy F. Walter, C. Titus Brown
2021 figshare.com  
We have designed hands-on lessons around bioinformatics tools that users can use to successfully find, access, and work with Common Fund data.  ...  Questions will be pulled from live workshop experience, and may also be sourced from questions sent in by users to the CFDE Training Help Desk.  ...  From in-lesson attendee feedback, observed problems, and data collected in pre and post-surveys, we addressed problems that arose in workshops to improve materials and methods in subsequent lessons.  ... 
doi:10.6084/m9.figshare.14588856.v1 fatcat:escyieopzfb4tasxoatgnjxgwq

The Bioinformatics Virtual Coordination Network: An Open-Source and Interactive Learning Environment

Benjamin J. Tully, Joy Buongiorno, Ashley B. Cohen, Jacob A. Cram, Arkadiy I. Garber, Sarah K. Hu, Arianna I. Krinos, Philip T. Leftwich, Alexis J. Marshall, Ella T. Sieradzki, Daan R. Speth, Elizabeth A Suter (+4 others)
2021 Frontiers in Education  
The BVCN was structured as an open-access resource with a central hub providing access to all lesson content and hands-on tutorials (https://biovcnet.github.io/).  ...  The goal of the Bioinformatics Virtual Coordination Network (BVCN) was to reduce some of these impacts by helping research biologists learn new skills and initiate computational projects as alternative  ...  their hands-on bioinformatics skills.  ... 
doi:10.3389/feduc.2021.711618 fatcat:v7glb3fngjetxn7quo34vie46q

The Bean Beetle Microbiome Project: A Course-Based Undergraduate Research Experience in Microbiology

Anna J. Zelaya, Nicole M. Gerardo, Lawrence S. Blumer, Christopher W. Beck
2020 Frontiers in Microbiology  
Course-based undergraduate research experiences (CUREs) are an effective means of transforming the learning and teaching of science by involving students in the scientific process.  ...  Additionally, students extract total DNA from beetle gut homogenates for high-throughput paired-end sequencing and perform bioinformatic and statistical analyses of bacterial communities using a combination  ...  A meaningful microbiome experiment will likely require a minimum of five samples in each of two treatments, or a total of 10 samples, so whole community sequencing will cost between $550 and $850/class  ... 
doi:10.3389/fmicb.2020.577621 pmid:33042093 pmcid:PMC7522406 fatcat:juthgsxdkjfifogst2ooogwvxu

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan (+4 others)
2019 F1000Research  
The de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.  ...  In addition to face-to-face training courses, online training was introduced on the de.NBI website in 2016 and guidelines for the preparation of e-learning material were established in 2018.  ...  and get hands-on experience of data analysis at the Data Carpentry workshops.  ... 
doi:10.12688/f1000research.20244.1 pmid:33163154 pmcid:PMC7607484 fatcat:g4gztfjahrbkdepxw6rgkjfhjy

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan (+4 others)
2020 F1000Research  
The de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.  ...  In addition to face-to-face training courses, online training was introduced on the de.NBI website in 2016 and guidelines for the preparation of e-learning material were established in 2018.  ...  and get hands-on experience of data analysis at the Data Carpentry workshops.  ... 
doi:10.12688/f1000research.20244.2 fatcat:io4rgsengvddhlhwjgpqv5livu

Second ISCB Latin American Student Council Symposium (LA-SCS) 2016

Alexander Miguel Monzon, Marcia A. Hasenahuer, Estefanía Mancini, Nilson Coimbra, Fiorella Cravero, Javier Cáceres-Molina, César A. Ramírez-Sarmiento, Nicolas Palopoli, Pieter Meysman, R. Gonzalo Parra
2017 F1000Research  
This report summarizes the scientific content and activities of the second edition of  ...  We greatly appreciate the support of International Society for Computational Biology (ISCB) and Argentinian Association for Computational Biology and Bioinformatics (A2B2C) for giving us the opportunity  ...  for his predisposition and assistance in organizing the LA-SCS 2016.  ... 
doi:10.12688/f1000research.12321.1 pmid:28928937 pmcid:PMC5580427 fatcat:hwulsofdorhbdm2dhusa2ccxj4

Diversifying the Genomic Data Science Research Community [article]

The Genomic Data Science Community Network, Rosa Alcazar
2022 arXiv   pre-print
Black Colleges and Universities, Hispanic-Serving Institutions, and Tribal Colleges and Universities in taking advantage of these tools in local educational and research programs.  ...  At the same time, there have been revolutions in cloud computing that enable computational and data science research, while making data accessible to anyone with a web browser and an internet connection  ...  This course will promote advanced scientific writing and broad perspectives of issues in current Bioinformatics research.  ... 
arXiv:2201.08443v2 fatcat:k3veowssp5e6hflp5f6hyhg75e

Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop

Fidele Ntie-Kang, Kiran K. Telukunta, Serge A. T. Fobofou, Victor Chukwudi Osamor, Samuel A. Egieyeh, Marilia Valli, Yannick Djoumbou-Feunang, Maria Sorokina, Conrad Stork, Neann Mathai, Paul Zierep, Ana L. Chávez-Hernández (+23 others)
2021 Journal of Cheminformatics  
The final program available on the workshop website (https://caismd.indiayouth.info/) comprised of 4 keynote lectures (KLs), 12 oral presentations (OPs), 2 round table discussions (RTDs), and 5 hands-on  ...  The invited experts gave keynote lectures, trained participants in hands-on sessions, and held round table discussions.  ...  The workshop lectures and materials shown and worked with during the hands-on sessions have been made available for download from the workshop website.  ... 
doi:10.1186/s13321-021-00546-8 pmid:34488889 fatcat:bris3urddngwpkwzgcgov7mqxy

HARNESSING BIG DATA FOR PRECISION MEDICINE: INFRASTRUCTURES AND APPLICATIONS

KUN-HSING YU, STEVEN N. HART, RACHEL GOLDFEDER, QIANGFENG CLIFF ZHANG, STEPHEN C. J. PARKER, MICHAEL SNYDER
2016 Biocomputing 2017  
Gustavo Stolovitzky (IBM) and Josh Swamidass (Washington University in St. Louis) to the preparation of this workshop summary.  ...  After earning her bachelor's degree in biology from Harvard, Dr.  ...  Two new areas of translational bioinformatics are microbiome and single cell genomics. Both fields have measurement uncertainty.  ... 
doi:10.1142/9789813207813_0058 pmid:27897013 fatcat:y3dbcwj5ire6dhblwd5oaniozy

Report of the 13th Genomic Standards Consortium Meeting, Shenzhen, China, March 4–7, 2012

Jack A. Gilbert, Yiming Bao, Hui Wang, Susanna-Assunta Sansone, Scott C. Edmunds, Norman Morrison, Folker Meyer, Lynn M. Schriml, Neil Davies, Peter Sterk, Jared Wilkening, George M. Garrity (+5 others)
2012 Standards in Genomic Sciences  
To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities.  ...  Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample.  ...  We thank Eppendorf, MoBio, BGI, Lucigen, and Hua Yue Enterprise Holdings Ltd. for their spon-sorship of the meeting. We also thank the Gordon and Betty Moore Foundation for support and the U.S.  ... 
doi:10.4056/sigs.2876184 pmid:22768370 pmcid:PMC3387801 fatcat:ysflrsim55dmpmrvbch4kxxl5u

Diversifying the genomic data science research community

Genomic Data Science Community Network
2022 biorxiv/medrxiv  
excellence, fostering student awareness, developing modular and open-source resources, expanding course-based undergraduate research experiences (CUREs), building curriculum, supporting student professional  ...  development and research, and removing financial barriers through funding programs and collaborator support.  ...  O'Connor Professor of Biology and Computer Science at Johns Hopkins University, who was one of the original architects of the AnVIL and an ardent champion for open science (https ://galaxyproject.org/jxtx  ... 
doi:10.1101/gr.276496.121 pmid:35858750 pmcid:PMC9341509 fatcat:u5xvbndl2jcbtfbchipp4utfea

Women in the European Virus Bioinformatics Center

Franziska Hufsky, Ana Abecasis, Patricia Agudelo-Romero, Magda Bletsa, Katherine Brown, Claudia Claus, Stefanie Deinhardt-Emmer, Li Deng, Caroline C. Friedel, María Inés Gismondi, Evangelia Georgia Kostaki, Denise Kühnert (+16 others)
2022 Viruses  
Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems.  ...  These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration  ...  Acknowledgments: We thank all members and especially the female members of the EVBC for their great work in advancing virus bioinformatics.  ... 
doi:10.3390/v14071522 pmid:35891501 pmcid:PMC9319252 fatcat:gq7oynyu7ngkpli5mkusnhiwia

BioData.pt | ELIXIR PT Annual Report 2021 [article]

Ana M. P. Melo, Pedro M. Barros, Daniel Faria, Jorge Oliveira, Inês Chaves
2022 figshare.com  
Have a look in our achievements and leave us your comments and suggestions.  ...  Here, ELIXIR efforts to demonstrate its public value and the lessons learned during the process are discussed for the benefit of other research organisations.  ...  One hundred and two companies had their core activity in biotechnology, 110 had their secondary activity in Biotechnology, and 10 were based on the Biocant Park.  ... 
doi:10.6084/m9.figshare.20117636.v2 fatcat:qqqr4wt6irhudhpggts3w3pvcu

BioData.pt | ELIXIR PT Annual Report 2021 [article]

Ana M. P. Melo, Pedro M. Barros, Daniel Faria, Jorge Oliveira, Inês Chaves
2022 figshare.com  
Have a look in our achievements and leave us your comments and suggestions.  ...  Here, ELIXIR efforts to demonstrate its public value and the lessons learned during the process are discussed for the benefit of other research organisations.  ...  One hundred and two companies had their core activity in biotechnology, 110 had their secondary activity in Biotechnology, and 10 were based on the Biocant Park.  ... 
doi:10.6084/m9.figshare.20117636.v1 fatcat:gnoncvc35jdirecbh7yiawpgem
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