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Reproducible Research with Word? | Eric P. Green

Reproducible Research with Word? | Eric P. Green | Reproducible OR | Scoop.it

Kieran Healy’s post describing his manuscript preparation workflow inspired me to write up some notes about how I approach some of the same challenges. Namely, other people.

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Reproducible OR
Reproducible Operations Research: making the application of advanced analytics to decision-making more credible.
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The Kitware Blog - Reproducible Research Book - Practicing Open Science

The Kitware Blog - Reproducible Research Book - Practicing Open Science | Reproducible OR | Scoop.it
Walking the Walk
Scott Nestler's insight:

The book features contributions under three major themes of

"Tools","Practices and Guidelines" and"Platforms"
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Reproducible Research with Roger D. Peng - YouTube

Sign up for "Reproducible Research" at http://www.coursera.org/course/repdata. This course, taught by Roger Peng, Jeff Leek, and Brian Caffo from Johns Hopki...
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Reproducibility in the age of Mechanical Turk: We’re not there yet

Reproducibility in the age of Mechanical Turk: We’re not there yet | Reproducible OR | Scoop.it
There’s been increasing interest in the computer science research community in exploring the reproducibility of our research findings. One such project recently received quite a bit of attention for...
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The Role of Data Repositories in Reproducible Research | Institution for Social and Policy Studies

The Role of Data Repositories in Reproducible Research | Institution for Social and Policy Studies | Reproducible OR | Scoop.it
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Software in your reproducible research

Software in your reproducible research | Reproducible OR | Scoop.it

Some thoughts from Dmitrijs Milajeves on "why reproducibility is a dream that easily becomes a nightmare."

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Reproducibility in data mining/learning

Is reproducibility in data mining/learning different from reproducibility in systems research ?

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▶ Panel: Rerun-ability, Repeatability, and Reproducibility in Experimentation - YouTube

The LASER 2013 Workshop Roy Maxion, CMU Terry Benzel, USC/ISI Lance G. Joneckis, IDA A panel of cyber security experimentation experts will discuss the conce...
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Implementing Reproducible Research (Chapman & Hall/CRC The R Series): Victoria Stodden, Friedrich Leisch, Roger D. Peng: 9781466561595: Amazon.com: Books

Implementing Reproducible Research (Chapman & Hall/CRC The R Series) [Victoria Stodden, Friedrich Leisch, Roger D. Peng] on Amazon.com. *FREE* shipping on qualifying offers. In computational science, reproducibility requires that researchers make code and data available to others so that the data can be analyzed in a similar manner as in the original publication. Code must be available to be distributed
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Science wins as PLoS goes hard on Open Access (Wired UK)

Science wins as PLoS goes hard on Open Access (Wired UK) | Reproducible OR | Scoop.it
Academic journal PLoS (Public Library of Science) has changed its policy so that authors are now required to make the data underlying their scientific findings available publicly
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To teach scientific reproducibility, start young

To teach scientific reproducibility, start young | Reproducible OR | Scoop.it
The ability to duplicate an experiment and its results is a central tenet of the scientific method, but recent research has shown an alarming number of peer-reviewed papers are irreproducible.
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Here’s why the scientific publishing system can never be “fixed” | Simply Statistics

Here’s why the scientific publishing system can never be “fixed” | Simply Statistics | Reproducible OR | Scoop.it

The scientific publishing system, as broken as you may find it to be, can never truly be fixed. Ultimately, in a universe where there are finite resources, a system has to be developed to determine how those resources should be distributed. Any system that we can come up with will be flawed as there will by necessity have to be winners and losers. I think there are serious efforts that need to be made to make the system more fair and more transparent, but the problem will never truly be "fixed" to everyone's satisfaction.

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Reproducible research, training wheels, and knitr

Reproducible research, training wheels, and knitr | Reproducible OR | Scoop.it
Last week I gave a short talk at CMU’s statistical computing seminar, Stat Bytes. I summarized why reproducible research (RR) and literate programming are worthwhile, not just for serious res...
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Collaborations Workshop 2014 (CW14) - software in your reproducible research | Software Sustainability Institute

Collaborations Workshop 2014 (CW14) - software in your reproducible research | Software Sustainability Institute | Reproducible OR | Scoop.it

The Software Sustainability Institute's annual Collaborations Workshop (CW14) brings together researchers, software developers, managers, funders and more to explore important ideas in software and research and to plant the seed of interdisciplinary collaborations.

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Some myths of reproducible computational research

Scott Nestler's insight:

"Six ways to Sunday: Approaches to computational reproducibility in non-model sequence analysis," contains list of five  "myths" of reproducible computational research: attitudes that wrongly discouraged people from actually doing computational research reproducibly.

 
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▶ Git That Data - YouTube

This is a video about a course offered at UC Berkeley called Stat 157: Reproducible and Collaborative Data Science You can read more about it here: https://g...
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Implementing Reproducible Research

Implementing Reproducible Research | Reproducible OR | Scoop.it
In computational science, reproducibility requires that researchers make code and data available to others so that the data can be analyzed in a similar manner…
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When it comes to scientific data, sharing is caring

When it comes to scientific data, sharing is caring | Reproducible OR | Scoop.it
Data sharing is crucial to scientific progress, and can ensure that valuable research isn’t lost
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Time for a scientific journal Reproducibility Index

Time for a scientific journal Reproducibility Index | Reproducible OR | Scoop.it

Reproducibility Index:  Rather than rate journals on how often their articles are cited by other researchers, let’s grade them on how well those papers stand the most important test of science: namely, does the work stand up to scrutiny?

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Reproducibility vs. usability

Reproducibility vs. usability | Reproducible OR | Scoop.it

Reproducibility has become a major issue in scientific publication, it is under scrutiny by many, making headlines in the news, is on the minds of journals, and there are guidelines for achieving it. Reproducibility is certainly important for scientific research, but I think that lost in the debate is the notion of usability.

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‘Data in Brief’ articles make reproducibility a reality

‘Data in Brief’ articles make reproducibility a reality | Reproducible OR | Scoop.it
The open access journal Genomics Data helps researchers make the most of their data
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A great idea: R Markdown for Undergrads

A great idea: R Markdown for Undergrads | Reproducible OR | Scoop.it
A recently published paper by Baumer et al (2014) caught my eye today (HT to Bruce Caron).  I wanted to share it here because I thought it was cool and also had a few comments to make about some of...
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About the Reproducibility Initiative

The aim of the Reproducibility Initiative is to identify and reward high quality reproducible research.

To identify reproducible research and reagents, key experimental results are independently validated using the Science Exchange network of experts.

Studies, protocols or reagents can be quickly and cost effectively independently validated by the Science Exchange network, which consists of more than 2000 laboratories from 400 research institutes. Submitted experiments are matched with an appropriate, verified lab who then reproduces the experiments. All submissions are confidential, with resultant data and findings kept private. Upon completion, all experimental results are provided to the submitter and permission to use the Reproducibility Initiative "independently validated" badge is provided.

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Reproducibility of research results: a subjective view | SciELO in Perspective

Reproducibility of research results: a subjective view | SciELO in Perspective | Reproducible OR | Scoop.it
At a time when discussions about ethics in experimentation and scientific publication are going beyond laboratories and academic environments, and are peaking the interest of society as a whole, another threat is emerging to the credibility of science. Irreproducibility of research results is affecting the different areas of knowledge and is of concern to all. The pressure on researchers for positive and high impact outcomes is bound up with the natural desire of scientists to make groundbreaking discoveries, even if the evidence points to the contrary.
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Git can facilitate greater reproducibility and increased transparency in science

Git, an open source version control system (VCS) provides a lightweight yet robust framework that is ideal for managing the full suite of research outputs such as datasets, statistical code, figures, lab notes, and manuscripts. For individual researchers, Git provides a powerful way to track and compare versions, retrace errors, explore new approaches in a structured manner, while maintaining a full audit trail. For larger collaborative efforts, Git and Git hosting services make it possible for everyone to work asynchronously and merge their contributions at any time, all the while maintaining a complete authorship trail. In this paper I provide an overview of Git along with use-cases that highlight how this tool can be leveraged to make science more reproducible and transparent, foster new collaborations, and support novel uses.

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The Billionaire Couple Targeting Shoddy and Secretive Science - Inside Philanthropy: Fundraising Intelligence - Inside Philanthropy

The Laura and John Arnold Foundation has a one-of-a-kind program to improve research integrity by increasing transparency and reliability of scientific studies.

The program’s signature grantee is the Center for Open Science, a project of psychologist Brian Nosek to improve openness and reproducibility of research. The center was established by the Arnold Foundation last year with a $5.25 million grant, and has received an additional $1.5 million for its efforts to test past studies by replicating them.

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