Foundational Open Science Skills Workshop Series:
Practical Data and Software Skills for Reproducible Research¶
Two introductory workshops on the skills and technologies you need for publishable and reproducible data-driven science
Working with “Big data” is challenging for most researchers and the barriers to publication can be difficult. These workshops introduce free open-source approaches that reduce these challenges and help you deliver research that is more impactful, open, and reproducible.
Training will focus on solutions developed by publicly funded cyberinfrastructure developed in the US (CyVerse) and Europe (CyVerse UK, ELIXIR, EOSC, and others). Lessons learned will prepare you with skills you can apply no matter which computing platforms you use.
Upcoming Workshops¶
Start this semester with the skills you need – from research and data management to publication!
Workshop Location
Rome, Italy - October 2019 (cancelled)
Host: University of Arkansas
Location: University of Arkansas Rome Center: Palazzo Taverna, Via di Monte Giordano, 36 - 00186 Rome Italy.
Dates: Each workshop will run from afternoon to afternoon (see Draft Agenda below for times)
- Practical Data Skills Workshop: October 2nd - October 3rd
- Practical Software Skills Workshop: October 3rd - October 4th
Costs/Funding/Registration: A fee of $40 US for each workshop ($80 US total if attending both) covers facility setup and administrative costs, as well as AM and PM refreshment breaks. Participants are responsible for all costs associated with their attendance (travel, lodging, meals, etc.). There will be an optional luncheon between the workshops on Thursday October 4 at a cost of $20 US.
Flyer:
Workshop Registration:
This Workshop has been cancelled
All attendees should have received refunds. Contact williams@cshl.edu for questions or problems.
Cancellations
In the event of insufficient enrollment, we reserve the right to cancel the workshops. We will confirm the workshop no later than 3 weeks prior to the start of the workshop (September 18th, 2019) or as soon as minimum enrollment is met. We strongly encourage you not to make non-refundable travel plans before you are notified the workshop is confirmed. In the event of a cancellation we will only refund your registration costs.
You may cancel your attendance at the workshop at any time, but full refunds may only be available until September 25th, 2019 (1 week prior to workshop start).
Workshop Audiences, Learning Outcomes, and Prerequisites¶
Practical Data Skills Workshop¶
Audience
Investigators and researchers working in all areas of the life sciences. Workshop delivery style will benefit those looking for information on and making decisions about these technologies (e.g. principal investigators, grant writers, funders/grant officers, etc.) but who may not actually use them day-to-day.
Learning Outcomes
At this workshop learners will:
- Identify common challenges for large/complex biological datasets
- Understand the value and application of FAIR/Open Science principles
- Gain skills for using free data sharing and data management technologies
- Create (or refine) a custom data management plan for their research
Prerequisites
This workshop is suitable for a non-technical audience. For computer labs, basic knowledge in working with spreadsheets (e.g. Excel) is helpful. Attendees must bring their own Wi-Fi enabled laptop.
Practical Software Skills Workshop¶
Audience
Investigators and researchers working in all areas of the life sciences. Workshop delivery style will benefit those looking for information on improving how they use software in their research - from simple scripts developed in-house to building robust, reproducible, and scalable, pipelines.
Learning Outcomes
At this workshop learners will:
- Identify common software reproducibility challenges
- Gain skills for using free reproducibility technologies like version control (git/GitHub), containerization (Docker), and notebooks (Jupyter)
- Learn how to deploy applications for reproducible analysis using MyBinder and CyVerse
- Create (or refine) a custom software management plan for your research
Prerequisites
This workshop will have several labs involving use of the command line (Linux/Unix). Some basic command line experience is strongly suggested. Attendees must bring their own Wi-Fi enabled laptop.
Agendas¶
Draft Agenda (subject to change)
Practical Data Skills Workshop: October 2nd - October 3rd
October 2nd
| Time | Topic | Objectives and Activities |
|---|---|---|
| 14:00 | Workshop overview and introduction to CyVerse - Technology for open science (lecture) | Brief overview of CyVerse (publicly funded infrastructure project) and how it is being adopted internationality (CyVerse UK/Austria/Australia), how you can make free use of it, and how these and other technologies are relevant to European bioinformatics and infrastructure projects (e.g. ELIXIR and EOSC). We will also introduce common tools and related vocabulary for computing in life science research. |
| 14:30 | FAIR in practice - Increasing the impact of your work through Open Science (lecture and interactive discussion) | Participants will get an introduction to the FAIR principles and an overview of some of the major community projects and technological approaches for implementing FAIR and complying with mandates such as Plan S. Key ideas and approaches to Open Science will be introduced. An interactive discussion on data management challenges will have participants work through sections of grant applications (their own and provided examples) to identify weak points in FAIRness. |
| 15:30 | Break | |
| 15:45 | Making data reusable and interoperable with metadata standards (lecture) | Participants will learn how community and repository standards can be selected and implemented for their own datasets. |
| 16:15 | Managing data with Open Refine (lab) | Using the free and open-source software Open Refine, participants will explore how metadata can be organized and validated to comply with their choice of metadata standards. |
| 18:00 | End of Day One |
October 3rd
| Time | Topic | Objectives and Activities |
|---|---|---|
| 9:00 | Associating data with Metadata (lab) | Users will be guided through associating metadata with data on the CyVerse platform using its graphical interface to iRODS (a data storage technology used by several international repositories) |
| 9:30 | Making data available through repositories (lecture) | We will introduce popular repositories and the typical requirements for publication of datasets including choices of licensing. |
| 10:00 | CyVerse Data Commons publication model (lab) | Participants will be guided through making data available and citable (DOI issuing) on the CyVerse data store. We will also demonstrate publication directly from CyVerse to NCBI and also ENA using COPO. |
| 10:30 | Break | |
| 10:45 | Increasing the value of your work with pre-prints and getting credit with data licensing (lecture) | We will discuss the evidence and some available solutions for making use of pre-prints and solutions for choosing a data license. |
| 11:15 | Making a data management plan work for you (lab and interactive discussion) | Participants will start to summarize lessons learned by completing a Data Stewardship wizard and generating an updated data management plan |
| 11:45 | Summary and Road mapping (lab and interactive discussion) | Participants will work in small teams to develop learning roadmaps to be implemented post-workshop (How will the workshop change what they are now doing? What questions do they still have? What technologies would the like more information on? etc.). These will be shared and collected and the instructional team will leave additional feedback and suggestions on the maps during and shortly after the workshop. |
| 13:30 | Finish (End of Workshop) | Lunch available (purchase ticket at Eventbrite link) |
13:30 October 3rd - Lunch will be available at the Workshop Venue: Eventbrite ticket purchase required.
Practical Software Skills Workshop: October 3rd - October 4th
October 3rd
| Time | Topic | Objectives and Activities |
|---|---|---|
| 14:30 | Workshop overview and Introduction to CyVerse - Technology for Open Science (lecture) | Brief overview of CyVerse (publicly funded infrastructure project) and how it is being adopted internationality (CyVerse UK/Austria/Australia), how you can make free use of it, and how these and other technologies are relevant to European bioinformatics and infrastructure projects (e.g. ELIXIR and EOSC). We will also introduce common tools and related vocabulary for computing in life science research. |
| 15:00 | 4OSS - Introduction to Open Source Software Principles (lecture) | Participants will learn about the 4OSS principles and how they support reproducible, high-impact science through sustainable software and computing choices. |
| 15:30 | Break | |
| 15:45 | Github for software management and reproducibility - a brief introduction to Github (lab) | Participants will get a brief introduction to repository creation in Github and learn the value of developing code that is open from day one. Introduction of licensing and recommendations for fostering and managing contributions. |
| 17:30 | Containers for Computing (lab) | Participants will be introduced to Docker as a solution for software reproducibility, portability, and management. We will cover the basics of Docker and describe the process of pulling and running containers, including from popular repositories such as docker hub and biocontainers. |
| 18:30 | End of Day One |
October 4th
| Time | Topic | Objectives and Activities |
|---|---|---|
| 9:00 | Managing applications in Notebooks (lab) | Participants will cover the use of Docker to manage applications to deploy applications and use Jupyter notebooks to interface with applications. |
| 10:30 | Break | |
| 11:15 | Deploying applications (lab) | Participants will take applications developed in the workshop and see how they can be deployed as usable applications in CyVerse as well as My Binder. |
| 13:30 | Summary and Road mapping (lab and interactive discussion) | Participants will work in small teams to develop learning roadmaps to be implemented post-workshop (How will the workshop change what they are now doing? What questions do they still have? What technologies would the like more information on? etc.). These will be shared and collected and the instructional team will leave additional feedback and suggestions on the maps during and shortly after the workshop. |
| 14:30 | Finish (End of Workshop) |
Pre-Workshop Setup¶
Detailed Instructions Coming Soon
Questions¶
For workshop content questions, please email Jason Williams (Cold Spring Harbor Laboratory, NY). Williams@cshl.edu.
Content/Instruction Contributions¶
If you are interested in helping to further develop this workshop content, please also contact Jason at the address above, including if you are interested in helping as a volunteer as a TA at the workshop (unfortunately no funding is available for volunteers).
For participants interested in adapting/teaching future versions of this workshop please also let us know - we will have informal post-workshop sessions to help plan and promote future activities.
Organizers, Content Developers, and Instructional Team, Rome 2019¶
Douglas Rhoads (Host)
University Professor of Biological Sciences Director, Cell and Molecular Biology Program University of Arkansas
Allegra Via
Institute for Molecular Biology and Pathology, The National Research Council of Italy
Jason Williams
Email (williams@cshl.edu)
*(Contact Jason for all workshop related questions)
Assistant Director, External Collaborations Cold Spring Harbor Laboratory, DNA Learning Center CyVerse Education Outreach and Training Lead
Robert Davey
Group Leader Earlham Institute
Fotis Psomopoulos
Research Assistant Professor Institute of Applied Biosciences (INAB) Center for Research and Technology Hellas (CERTH)
Mateusz Kuzak
Netherlands eScience Center
Ramona L. Walls
Senior Scientific Analyst, CyVerse Assistant Research Professor, Bio5 Institute University of Arizona
About CyVerse¶
CyVerse Vision: Transforming science through data-driven discovery.
CyVerse Mission: Design, deploy, and expand a national cyberinfrastructure for life sciences research and train scientists in its use. CyVerse provides life scientists with powerful computational infrastructure to handle huge datasets and complex analyses, thus enabling data-driven discovery. Our powerful extensible platforms provide data storage, bioinformatics tools, image analyses, cloud services, APIs, and more.
While originally created with the name iPlant Collaborative to serve U.S. plant science communities, CyVerse cyberinfrastructure is germane to all life sciences disciplines and works equally well on data from plants, animals, or microbes. By democratizing access to supercomputing capabilities, we provide a crucial resource to enable scientists to find solutions for the future. CyVerse is of, by, and for the community, and community-driven needs shape our mission. We rely on your feedback to provide the infrastructure you need most to advance your science, development, and educational agenda.
CyVerse Homepage: http://www.cyverse.org
Funding and Citations¶
CyVerse is funded entirely by the National Science Foundation under Award Numbers DBI-0735191 and DBI-1265383.
Please cite CyVerse appropriately when you make use of our resources, CyVerse citation policy