This document discusses reproducible research and provides guidance on key practices and tools to support reproducibility. It defines reproducibility as distributing all data, code, and tools required to reproduce published research results. Version control systems like Git allow researchers to track changes over time and collaborate more effectively. Tools like DMPTool can help researchers create data management plans and plan for long-term storage and sharing of research data and materials. R Markdown allows integrating human-readable text with executable code to produce reproducible reports and analyses.
What is reproducible research? Why should I use it? what tools should I use? This session will show you how to use scripts, version control and markdown to do better research.
Datat and donuts: how to write a data management planC. Tobin Magle
Good data management practices are becoming increasingly important in the digital age. Because we now have the technology to freely share research data and also because funding agencies want to do more with decreasing research funds, many funding agencies and journals require authors and grantees to share their research data. To provide training in this area, Tobin Magle, the Morgan Library's Cyberinfrastructure Facilitator, is putting on a series of data management workshops called "Data and Donuts". The first session of Data and Donuts will discuss the importance of data management and how to write a data management plan.
This session covers topics related to data archiving and sharing. This includes data formats, metadata, controlled vocabularies, preservation, archiving and repositories.
Data and Donuts: How to write a data management planC. Tobin Magle
This presentation describes best practices for how to write a data management plan for your research data. Additionally, it provides information about finding funder requirements, metadata standards, and repositories.
What is reproducible research? Why should I use it? what tools should I use? This session will show you how to use scripts, version control and markdown to do better research.
Datat and donuts: how to write a data management planC. Tobin Magle
Good data management practices are becoming increasingly important in the digital age. Because we now have the technology to freely share research data and also because funding agencies want to do more with decreasing research funds, many funding agencies and journals require authors and grantees to share their research data. To provide training in this area, Tobin Magle, the Morgan Library's Cyberinfrastructure Facilitator, is putting on a series of data management workshops called "Data and Donuts". The first session of Data and Donuts will discuss the importance of data management and how to write a data management plan.
This session covers topics related to data archiving and sharing. This includes data formats, metadata, controlled vocabularies, preservation, archiving and repositories.
Data and Donuts: How to write a data management planC. Tobin Magle
This presentation describes best practices for how to write a data management plan for your research data. Additionally, it provides information about finding funder requirements, metadata standards, and repositories.
Presentation given at Organization for Human Brain Mapping Annual Meeting in Singapore 2018
Video recording: https://www.pathlms.com/ohbm/courses/8246/sections/12538/video_presentations/116214
Written and presented by Tom Ingraham (F1000), at the Reproducible and Citable Data and Model Workshop, in Warnemünde, Germany. September 14th -16th 2015.
Open Harvester - Search publications for a researcher from CrossRef, PubMed a...Muhammad Javed
A java prototype that processes the result set of pre-downloaded data (from a database) and allows one to claim his/her publications from a ranked list.
The Royal Society of Chemistry publishes many thousands of articles per year, the majority of these containing rich chemistry data that, in general, in limited in its value when isolated only to the HTML or PDF form of the articles commonly consumed by readers. RSC also has an archive of over 300,000 articles containing rich chemistry data especially in the form of chemicals, reactions, property data and analytical spectra. RSC is developing a platform integrating these various forms of chemistry data. The data will be aggregated both during the manuscript deposition process as well as the result of text-mining and extraction of data from across the RSC archive. This presentation will report on the development of the platform including our success in extracting compounds, reactions and spectral data from articles. We will also discuss our developing process for handling data at manuscript deposition and the integration and support of eLab Notebooks (ELNS) in terms of facilitating data deposition and sourcing data. Each of these processes is intended to ensure long-term access to research data with the intention of facilitating improved discovery.
The Royal Society of Chemistry was pleased to contribute to the Open PHACTS project, a 3 year project funded by the Innovative Medicines Initiative fund from the European Union. For three years we developed our existing platforms, created new and innovative widgets and data platforms to handle chemistry data, extended existing chemistry ontologies and embraced the semantic web open standards. As a result RSC served as the centralized chemistry data hub for the project. With the conclusion of the Open PHACTS project we will report on our experiences resulting from our participation in the project and provide an overview of what tools, capabilities and data have been released into the community as a result of our participation and how this may influence future projects. This will include the Open PHACTS open chemistry data dump including the chemistry related data in chemistry and semantic web consumable formats as well as some of the resulting chemistry software released to the community. The Open PHACTS project resulted in significant contributions to the chemistry community as well as the supporting pharmaceutical companies and biomedical community.
Being Reproducible: SSBSS Summer School 2017Carole Goble
Lecture 2:
Being Reproducible: Models, Research Objects and R* Brouhaha
Reproducibility is a R* minefield, depending on whether you are testing for robustness (rerun), defence (repeat), certification (replicate), comparison (reproduce) or transferring between researchers (reuse). Different forms of "R" make different demands on the completeness, depth and portability of research. Sharing is another minefield raising concerns of credit and protection from sharp practices.
In practice the exchange, reuse and reproduction of scientific experiments is dependent on bundling and exchanging the experimental methods, computational codes, data, algorithms, workflows and so on along with the narrative. These "Research Objects" are not fixed, just as research is not “finished”: the codes fork, data is updated, algorithms are revised, workflows break, service updates are released. ResearchObject.org is an effort to systematically support more portable and reproducible research exchange.
In this talk I will explore these issues in more depth using the FAIRDOM Platform and its support for reproducible modelling. The talk will cover initiatives and technical issues, and raise social and cultural challenges.
FAIRDOM - FAIR Asset management and sharing experiences in Systems and Synthe...Carole Goble
Over the past 5 years we have seen a change in expectations for the management of all the outcomes of research – that is the “assets” of data, models, codes, SOPs and so forth. Don’t stop reading. Data management isn’t likely to win anyone a Nobel prize. But publications should be supported and accompanied by data, methods, procedures, etc. to assure reproducibility of results. Funding agencies expect data (and increasingly software) management retention and access plans as part of the proposal process for projects to be funded. Journals are raising their expectations of the availability of data and codes for pre- and post- publication. The multi-component, multi-disciplinary nature of Systems Biology demands the interlinking and exchange of assets and the systematic recording
of metadata for their interpretation.
The FAIR Guiding Principles for scientific data management and stewardship (http://www.nature.com/articles/sdata201618) has been an effective rallying-cry for EU and USA Research Infrastructures. FAIRDOM (Findable, Accessible, Interoperable, Reusable Data, Operations and Models) Initiative has 8 years of experience of asset sharing and data infrastructure ranging across European programmes (SysMO and EraSysAPP ERANets), national initiatives (de.NBI, German Virtual Liver Network, UK SynBio centres) and PI's labs. It aims to support Systems and Synthetic Biology researchers with data and model management, with an emphasis on standards smuggled in by stealth and sensitivity to asset sharing and credit anxiety.
This talk will use the FAIRDOM Initiative to discuss the FAIR management of data, SOPs, and models for Sys Bio, highlighting the challenges of and approaches to sharing, credit, citation and asset infrastructures in practice. I'll also highlight recent experiments in affecting sharing using behavioural interventions.
http://www.fair-dom.org
http://www.fairdomhub.org
http://www.seek4science.org
Presented at COMBINE 2016, Newcastle, 19 September.
http://co.mbine.org/events/COMBINE_2016
What is Reproducibility? The R* brouhaha (and how Research Objects can help)Carole Goble
presented at 1st First International Workshop on Reproducible Open Science @ TPDL, 9 Sept 2016, Hannover, Germany
http://repscience2016.research-infrastructures.eu/
Being FAIR: FAIR data and model management SSBSS 2017 Summer SchoolCarole Goble
Lecture 1:
Being FAIR: FAIR data and model management
In recent years we have seen a change in expectations for the management of all the outcomes of research – that is the “assets” of data, models, codes, SOPs, workflows. The “FAIR” (Findable, Accessible, Interoperable, Reusable) Guiding Principles for scientific data management and stewardship [1] have proved to be an effective rallying-cry. Funding agencies expect data (and increasingly software) management retention and access plans. Journals are raising their expectations of the availability of data and codes for pre- and post- publication. The multi-component, multi-disciplinary nature of Systems and Synthetic Biology demands the interlinking and exchange of assets and the systematic recording of metadata for their interpretation.
Our FAIRDOM project (http://www.fair-dom.org) supports Systems Biology research projects with their research data, methods and model management, with an emphasis on standards smuggled in by stealth and sensitivity to asset sharing and credit anxiety. The FAIRDOM Platform has been installed by over 30 labs or projects. Our public, centrally hosted Asset Commons, the FAIRDOMHub.org, supports the outcomes of 50+ projects.
Now established as a grassroots association, FAIRDOM has over 8 years of experience of practical asset sharing and data infrastructure at the researcher coal-face ranging across European programmes (SysMO and ERASysAPP ERANets), national initiatives (Germany's de.NBI and Systems Medicine of the Liver; Norway's Digital Life) and European Research Infrastructures (ISBE) as well as in PI's labs and Centres such as the SynBioChem Centre at Manchester.
In this talk I will show explore how FAIRDOM has been designed to support Systems Biology projects and show examples of its configuration and use. I will also explore the technical and social challenges we face.
I will also refer to European efforts to support public archives for the life sciences. ELIXIR (http:// http://www.elixir-europe.org/) the European Research Infrastructure of 21 national nodes and a hub funded by national agreements to coordinate and sustain key data repositories and archives for the Life Science community, improve access to them and related tools, support training and create a platform for dataset interoperability. As the Head of the ELIXIR-UK Node and co-lead of the ELIXIR Interoperability Platform I will show how this work relates to your projects.
[1] Wilkinson et al, The FAIR Guiding Principles for scientific data management and stewardship Scientific Data 3, doi:10.1038/sdata.2016.18
Presentation given at Organization for Human Brain Mapping Annual Meeting in Singapore 2018
Video recording: https://www.pathlms.com/ohbm/courses/8246/sections/12538/video_presentations/116214
Written and presented by Tom Ingraham (F1000), at the Reproducible and Citable Data and Model Workshop, in Warnemünde, Germany. September 14th -16th 2015.
Open Harvester - Search publications for a researcher from CrossRef, PubMed a...Muhammad Javed
A java prototype that processes the result set of pre-downloaded data (from a database) and allows one to claim his/her publications from a ranked list.
The Royal Society of Chemistry publishes many thousands of articles per year, the majority of these containing rich chemistry data that, in general, in limited in its value when isolated only to the HTML or PDF form of the articles commonly consumed by readers. RSC also has an archive of over 300,000 articles containing rich chemistry data especially in the form of chemicals, reactions, property data and analytical spectra. RSC is developing a platform integrating these various forms of chemistry data. The data will be aggregated both during the manuscript deposition process as well as the result of text-mining and extraction of data from across the RSC archive. This presentation will report on the development of the platform including our success in extracting compounds, reactions and spectral data from articles. We will also discuss our developing process for handling data at manuscript deposition and the integration and support of eLab Notebooks (ELNS) in terms of facilitating data deposition and sourcing data. Each of these processes is intended to ensure long-term access to research data with the intention of facilitating improved discovery.
The Royal Society of Chemistry was pleased to contribute to the Open PHACTS project, a 3 year project funded by the Innovative Medicines Initiative fund from the European Union. For three years we developed our existing platforms, created new and innovative widgets and data platforms to handle chemistry data, extended existing chemistry ontologies and embraced the semantic web open standards. As a result RSC served as the centralized chemistry data hub for the project. With the conclusion of the Open PHACTS project we will report on our experiences resulting from our participation in the project and provide an overview of what tools, capabilities and data have been released into the community as a result of our participation and how this may influence future projects. This will include the Open PHACTS open chemistry data dump including the chemistry related data in chemistry and semantic web consumable formats as well as some of the resulting chemistry software released to the community. The Open PHACTS project resulted in significant contributions to the chemistry community as well as the supporting pharmaceutical companies and biomedical community.
Being Reproducible: SSBSS Summer School 2017Carole Goble
Lecture 2:
Being Reproducible: Models, Research Objects and R* Brouhaha
Reproducibility is a R* minefield, depending on whether you are testing for robustness (rerun), defence (repeat), certification (replicate), comparison (reproduce) or transferring between researchers (reuse). Different forms of "R" make different demands on the completeness, depth and portability of research. Sharing is another minefield raising concerns of credit and protection from sharp practices.
In practice the exchange, reuse and reproduction of scientific experiments is dependent on bundling and exchanging the experimental methods, computational codes, data, algorithms, workflows and so on along with the narrative. These "Research Objects" are not fixed, just as research is not “finished”: the codes fork, data is updated, algorithms are revised, workflows break, service updates are released. ResearchObject.org is an effort to systematically support more portable and reproducible research exchange.
In this talk I will explore these issues in more depth using the FAIRDOM Platform and its support for reproducible modelling. The talk will cover initiatives and technical issues, and raise social and cultural challenges.
FAIRDOM - FAIR Asset management and sharing experiences in Systems and Synthe...Carole Goble
Over the past 5 years we have seen a change in expectations for the management of all the outcomes of research – that is the “assets” of data, models, codes, SOPs and so forth. Don’t stop reading. Data management isn’t likely to win anyone a Nobel prize. But publications should be supported and accompanied by data, methods, procedures, etc. to assure reproducibility of results. Funding agencies expect data (and increasingly software) management retention and access plans as part of the proposal process for projects to be funded. Journals are raising their expectations of the availability of data and codes for pre- and post- publication. The multi-component, multi-disciplinary nature of Systems Biology demands the interlinking and exchange of assets and the systematic recording
of metadata for their interpretation.
The FAIR Guiding Principles for scientific data management and stewardship (http://www.nature.com/articles/sdata201618) has been an effective rallying-cry for EU and USA Research Infrastructures. FAIRDOM (Findable, Accessible, Interoperable, Reusable Data, Operations and Models) Initiative has 8 years of experience of asset sharing and data infrastructure ranging across European programmes (SysMO and EraSysAPP ERANets), national initiatives (de.NBI, German Virtual Liver Network, UK SynBio centres) and PI's labs. It aims to support Systems and Synthetic Biology researchers with data and model management, with an emphasis on standards smuggled in by stealth and sensitivity to asset sharing and credit anxiety.
This talk will use the FAIRDOM Initiative to discuss the FAIR management of data, SOPs, and models for Sys Bio, highlighting the challenges of and approaches to sharing, credit, citation and asset infrastructures in practice. I'll also highlight recent experiments in affecting sharing using behavioural interventions.
http://www.fair-dom.org
http://www.fairdomhub.org
http://www.seek4science.org
Presented at COMBINE 2016, Newcastle, 19 September.
http://co.mbine.org/events/COMBINE_2016
What is Reproducibility? The R* brouhaha (and how Research Objects can help)Carole Goble
presented at 1st First International Workshop on Reproducible Open Science @ TPDL, 9 Sept 2016, Hannover, Germany
http://repscience2016.research-infrastructures.eu/
Being FAIR: FAIR data and model management SSBSS 2017 Summer SchoolCarole Goble
Lecture 1:
Being FAIR: FAIR data and model management
In recent years we have seen a change in expectations for the management of all the outcomes of research – that is the “assets” of data, models, codes, SOPs, workflows. The “FAIR” (Findable, Accessible, Interoperable, Reusable) Guiding Principles for scientific data management and stewardship [1] have proved to be an effective rallying-cry. Funding agencies expect data (and increasingly software) management retention and access plans. Journals are raising their expectations of the availability of data and codes for pre- and post- publication. The multi-component, multi-disciplinary nature of Systems and Synthetic Biology demands the interlinking and exchange of assets and the systematic recording of metadata for their interpretation.
Our FAIRDOM project (http://www.fair-dom.org) supports Systems Biology research projects with their research data, methods and model management, with an emphasis on standards smuggled in by stealth and sensitivity to asset sharing and credit anxiety. The FAIRDOM Platform has been installed by over 30 labs or projects. Our public, centrally hosted Asset Commons, the FAIRDOMHub.org, supports the outcomes of 50+ projects.
Now established as a grassroots association, FAIRDOM has over 8 years of experience of practical asset sharing and data infrastructure at the researcher coal-face ranging across European programmes (SysMO and ERASysAPP ERANets), national initiatives (Germany's de.NBI and Systems Medicine of the Liver; Norway's Digital Life) and European Research Infrastructures (ISBE) as well as in PI's labs and Centres such as the SynBioChem Centre at Manchester.
In this talk I will show explore how FAIRDOM has been designed to support Systems Biology projects and show examples of its configuration and use. I will also explore the technical and social challenges we face.
I will also refer to European efforts to support public archives for the life sciences. ELIXIR (http:// http://www.elixir-europe.org/) the European Research Infrastructure of 21 national nodes and a hub funded by national agreements to coordinate and sustain key data repositories and archives for the Life Science community, improve access to them and related tools, support training and create a platform for dataset interoperability. As the Head of the ELIXIR-UK Node and co-lead of the ELIXIR Interoperability Platform I will show how this work relates to your projects.
[1] Wilkinson et al, The FAIR Guiding Principles for scientific data management and stewardship Scientific Data 3, doi:10.1038/sdata.2016.18
The Basics of Open Source Collaboration With Git and GitHubBigBlueHat
A revised/minimized version of Nick Quaranto's (http://www.slideshare.net/qrush ) presentation on the same topic. This revised version was used to present Git to a group of students at ECPI who were not yet familiar with the concepts of version control or Git.
Git 101 - Crash Course in Version Control using GitGeoff Hoffman
Find out why more and more developers are switching to Git - distributed version control. This intro to Git covers the basics, from cloning to pushing for beginners.
[2015/2016] Collaborative software development with GitIvano Malavolta
This presentation is about a lecture I gave within the "Software systems and services" immigration course at the Gran Sasso Science Institute, L'Aquila (Italy): http://cs.gssi.infn.it/.
http://www.ivanomalavolta.com
This lecture is the first part of an introduction to SVC tools with a focus on Git and GitHub. This Lecture discusses the basic concepts as well as Installation and initial configuration of Git
Reproducible data science: review of Pachyderm, Data Version Control and GIT ...Josh Levy-Kramer
The advances in machine learning are great, yet, in order to have real value within a company, data scientists must be able to go from a research project to a reproducible process. A common problem is that the code is intrinsically linked to the data it was developed against. Hence it is critically important to track, trace and validate the input data used to train and test the algorithm. This talk will be a review of the several tools which for data versioning and processing.
Are you interesting in offering data management services at your library but aren’t sure where to start? Then this class is for you! During this session, we will
• Outline the data management topics that are commonly offered in libraries
• Present strategies for how to determine what services might be most useful on your campus and create synergistic partnerships with other university entities
• Dive into how to offer support with data management plans
• Present a case study for using an institutional repository to archive and share research data
• Identify additional training opportunities and open educational resources you can use to develop robust DM services
The class will consist of a mix of presentations, hands on activities, and discussion. So come ready to participate!
Data is getting bigger and more complex than ever before. Why not learn how to automate your analyses using the R programming language? This sessions covers the basics of using R such as operators, functions, data frames and factors.
Learn how to manipulate data frames using the dplyr package by Hadley Wickham. This session will cover select, filter, summarize, tally, group_by, and mutate. Based on the data carpentry ecology lessons
Data and donuts: Data Visualization using RC. Tobin Magle
Based on the Data Carpentry Curriculum, this presentation goes over how to visualize data in R using ggplot2 and enough data wrangling with dplyr to do it.
Responsible conduct of research: Data ManagementC. Tobin Magle
A presentation for the Food and Nutrition Science Responsible conduct of research class on data management best practices. Covers material in the context of writing a data management plan.
Data management is a key skill in the age of large, complex data sets. Collaborative research makes the process of managing research data harder. This presentation will cover some key features of the Open Science Framework that facilitate collaborative research.
Data and Donuts: The Impact of Data ManagementC. Tobin Magle
Good data management practices are becoming increasingly important in the digital age. Because we now have the technology to freely share research data and also because funding agencies want to do more with decreasing research funds, many funding agencies and journals require authors and grantees to share their research data. To provide training in this area, Tobin Magle, the Morgan Library's Data Management Specialist, is putting on a series of data management workshops called "Data and Donuts". Join us to learn about data management topics throughout the research data lifecycle.
Funding agencies are instituting requirements for data management and sharing as a condition of receiving research funds. This presentation addresses why researchers should care about research data management, what libraries have to do with it, and a case study of what one research specialist at the University of Colorado Anschutz Medical Campus is doing in this area.
Opendatabay - Open Data Marketplace.pptxOpendatabay
Opendatabay.com unlocks the power of data for everyone. Open Data Marketplace fosters a collaborative hub for data enthusiasts to explore, share, and contribute to a vast collection of datasets.
First ever open hub for data enthusiasts to collaborate and innovate. A platform to explore, share, and contribute to a vast collection of datasets. Through robust quality control and innovative technologies like blockchain verification, opendatabay ensures the authenticity and reliability of datasets, empowering users to make data-driven decisions with confidence. Leverage cutting-edge AI technologies to enhance the data exploration, analysis, and discovery experience.
From intelligent search and recommendations to automated data productisation and quotation, Opendatabay AI-driven features streamline the data workflow. Finding the data you need shouldn't be a complex. Opendatabay simplifies the data acquisition process with an intuitive interface and robust search tools. Effortlessly explore, discover, and access the data you need, allowing you to focus on extracting valuable insights. Opendatabay breaks new ground with a dedicated, AI-generated, synthetic datasets.
Leverage these privacy-preserving datasets for training and testing AI models without compromising sensitive information. Opendatabay prioritizes transparency by providing detailed metadata, provenance information, and usage guidelines for each dataset, ensuring users have a comprehensive understanding of the data they're working with. By leveraging a powerful combination of distributed ledger technology and rigorous third-party audits Opendatabay ensures the authenticity and reliability of every dataset. Security is at the core of Opendatabay. Marketplace implements stringent security measures, including encryption, access controls, and regular vulnerability assessments, to safeguard your data and protect your privacy.
StarCompliance is a leading firm specializing in the recovery of stolen cryptocurrency. Our comprehensive services are designed to assist individuals and organizations in navigating the complex process of fraud reporting, investigation, and fund recovery. We combine cutting-edge technology with expert legal support to provide a robust solution for victims of crypto theft.
Our Services Include:
Reporting to Tracking Authorities:
We immediately notify all relevant centralized exchanges (CEX), decentralized exchanges (DEX), and wallet providers about the stolen cryptocurrency. This ensures that the stolen assets are flagged as scam transactions, making it impossible for the thief to use them.
Assistance with Filing Police Reports:
We guide you through the process of filing a valid police report. Our support team provides detailed instructions on which police department to contact and helps you complete the necessary paperwork within the critical 72-hour window.
Launching the Refund Process:
Our team of experienced lawyers can initiate lawsuits on your behalf and represent you in various jurisdictions around the world. They work diligently to recover your stolen funds and ensure that justice is served.
At StarCompliance, we understand the urgency and stress involved in dealing with cryptocurrency theft. Our dedicated team works quickly and efficiently to provide you with the support and expertise needed to recover your assets. Trust us to be your partner in navigating the complexities of the crypto world and safeguarding your investments.
Explore our comprehensive data analysis project presentation on predicting product ad campaign performance. Learn how data-driven insights can optimize your marketing strategies and enhance campaign effectiveness. Perfect for professionals and students looking to understand the power of data analysis in advertising. for more details visit: https://bostoninstituteofanalytics.org/data-science-and-artificial-intelligence/
Adjusting primitives for graph : SHORT REPORT / NOTESSubhajit Sahu
Graph algorithms, like PageRank Compressed Sparse Row (CSR) is an adjacency-list based graph representation that is
Multiply with different modes (map)
1. Performance of sequential execution based vs OpenMP based vector multiply.
2. Comparing various launch configs for CUDA based vector multiply.
Sum with different storage types (reduce)
1. Performance of vector element sum using float vs bfloat16 as the storage type.
Sum with different modes (reduce)
1. Performance of sequential execution based vs OpenMP based vector element sum.
2. Performance of memcpy vs in-place based CUDA based vector element sum.
3. Comparing various launch configs for CUDA based vector element sum (memcpy).
4. Comparing various launch configs for CUDA based vector element sum (in-place).
Sum with in-place strategies of CUDA mode (reduce)
1. Comparing various launch configs for CUDA based vector element sum (in-place).
Chatty Kathy - UNC Bootcamp Final Project Presentation - Final Version - 5.23...John Andrews
SlideShare Description for "Chatty Kathy - UNC Bootcamp Final Project Presentation"
Title: Chatty Kathy: Enhancing Physical Activity Among Older Adults
Description:
Discover how Chatty Kathy, an innovative project developed at the UNC Bootcamp, aims to tackle the challenge of low physical activity among older adults. Our AI-driven solution uses peer interaction to boost and sustain exercise levels, significantly improving health outcomes. This presentation covers our problem statement, the rationale behind Chatty Kathy, synthetic data and persona creation, model performance metrics, a visual demonstration of the project, and potential future developments. Join us for an insightful Q&A session to explore the potential of this groundbreaking project.
Project Team: Jay Requarth, Jana Avery, John Andrews, Dr. Dick Davis II, Nee Buntoum, Nam Yeongjin & Mat Nicholas
2. Reproducibility
is the practice of distributing all data,
software source code, and tools required
to reproduce the results discussed in a
research publication.
https://www.ctspedia.org/do/view/CTSpedia/ReproducibleResearchStandards
3. Replication vs. Reproducibility
• Replication: The confirmation of results and conclusions from one study
obtained independently in another is considered the scientific gold standard.
• “Again, and Again, and Again …” BR Jasny et. al. Science, 2011. 334(6060) pp. 1225 DOI: 10.1126/science.334.6060.1225
• Some studies can’t be replicated: too big, too costly, too time consuming, one
time event, rare samples
• Reproducibility: minimum standard for assessing the value of scientific claims,
particularly when full independent replication of a study is not feasible
• “Reproducible Research in Computational Science”. RD Peng Science, 2011. 334 (6060) pp. 1226-1227 DOI: 10.1126/science.1213847
6. Requires new expertise and infrastructure
Form
Hypothesis
Collect
Data
Design
Experiment
Publish
research
Clean
Data
Analyze
Data
Write
manuscript
Share
data
Curate
data
Plan for data
storage
Data
Management
Plans
Version
control
Literate
Statistical
Computing
Reproducible
research
tools
7. DMPTool
• Developed by California Digital Libraries to help researchers write
data management plans
• https://dmptool.org/user_sessions/institution
• Select University of Colorado Anschutz Medical Campus
8. Create an account* or signin
*We’re working with OIT to allow us to log in with CU passport credentials. Stay tuned
10. Data management exercise
• Create a DMPTool account
• Pick a template and create a DMP
• Take 5 minutes to click through the template and think about how
these questions relate to your research
11. Version control
Version control is a system that records changes to a file or set of files
over time so that you can recall specific versions later.
https://git-scm.com/doc
13. Local version control system
Figure 1-1. Local version control.
https://git-scm.com/book/en/v2/Getting-Started-About-Version-Control
But what if you
need to collaborate?
• Keeps files in one place
• No copies
• Keeps track of changes
• Like Apple’s Time machine
16. What is Git?
• Distributed version control system developed by the Linux community
• A stream of snapshots
Figure 1-5. Storing data as snapshots of the project over time.
https://git-scm.com/book/en/v2/Getting-Started-Git-Basics
17. 3 states of repository files
• Modified – the file is altered but not committed
• Staged – the file is altered and marked to go to the next commit
• Committed- the file is altered and stored in your local DB
18. 3 Sections of your directory
Figure 1-6. Working directory, staging area, and Git directory.
https://git-scm.com/book/en/v2/Getting-Started-Git-Basics
Committed
Modified
Staged
19. Important git commands
• Init (Initialize) – start a git repository
• Add – add files to the git repository (for initial add and staging), can
be skipped with –a command
• Commit – safely store the files in your git repository
• Clone – make a copy of someone else’s git repository
20. File statuses and how they change
Figure 2-1. The lifecycle of the status of your files.
https://git-scm.com/book/en/v2/Git-Basics-Recording-Changes-to-the-Repository
27. Cloning/Branching/Forking
• Cloning: make a local copy of a repository online or elsewhere
• Branching: creating a separate stream to test new features, so you
don’t affect the “trunk”; branches depend on the trunk
• Collaboration
• Forking: Making a separate copy of a repository that is not dependent
• Using others’ work is a starting point; preserving things that the owner might
delete for yourself
33. Exercise
• Go to the repository you cloned earlier
• Create a text file with your name on it
• Add it to the name folder
• Submit a pull request
• Look at what happens to the visual representation
34. Literate (statistical) programming
• Resulting report is a stream of text (human readable) and code
(machine readable)
• Alternate text and code
• Sweave
• R markdown
35. R Markdown
• Open
• Write
• Embed
• Render
https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf
36. Install knitr and markdown packages
• Tools > install packages
• Enter the package name (will autocomplete)
• Knitr
• Markdown
• OR install.packages("knitr”)
• If it fails, try again
38. Write: useful syntax
• Plain text
• *italics* -> italics
• **bold** -> bold
• #Header -> Header (more # decreases size)
• Can also draw:
• Insert pictures
• Ordered and unordered list
• Tables
39. Embed code
• Inline – Use variables in the human readable text
• `r 2 + 2`
• Code chunks - Include working code that generates output
• ```{r}
• #Code goes here
• ```
• Display Options –
40. Render
• Won’t render unless the code runs with no errors
• You know it should be reproducible
• Render using the knit function
• Output Formats
• Knit HTML
• Knit PDF – requires latex
• Knit Word
41. Exercise
• Edit the markdown document using the cheat sheet to see what you
can do
• Try to knit it after creating a typo in the code
• Insert other pictures from the web
• Try to make a table
• Make some bulleted lists
• Insert a block quote
• Make the graph prettier
• Play around!
Editor's Notes
What issues do you see with the feasibility of this process?
These services span the research data lifecycle
Plan what you’re going to do with your data before you generate it
Curate and manage during collection
Temporary storage
Prepare for long term storage
Sharing optional (for now)
These services span the research data lifecycle
Plan what you’re going to do with your data before you generate it
Curate and manage during collection
Temporary storage
Prepare for long term storage
Sharing optional (for now)
Expertise and infrastructure
These services span the research data lifecycle
Plan what you’re going to do with your data before you generate it
Curate and manage during collection
Temporary storage
Prepare for long term storage
Sharing optional (for now)
Expertise and infrastructure