- May 2018
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www.nature.com www.nature.com
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Before reproducibility must come preproducibility
This article touches on many components of the repronim project.
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group.springernature.com group.springernature.com
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Researchers’ challenges in sharing data cross geographic borders and disciplines
Another report on challenges in data sharing.
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- Feb 2018
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courses.washington.edu courses.washington.edu
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Workshop Details August 20 – September 4, 2016 Friday Harbor Laboratories
Summer Workshop on the Dynamic Brain; August 18 – September 2, 2018; Friday Harbor, WA
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fluxsatellite.web.unc.edu fluxsatellite.web.unc.edu
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Big Data, Little Brains; May 6-8, 2018; UNC Chapel Hill
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www.nitrc.org www.nitrc.org
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empowering users to make local changes.
Local changes are great for customizability, but, it can play some havoc with reliability and reproducibility. 'ReproNim' recommends making such custom changes under the control of a version management system (ie. GitHub) so that the user can document an exact version of analysis used.
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- Jan 2018
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www.nlm.nih.gov www.nlm.nih.gov
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github.com github.com
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openrefine.org openrefine.org
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neurodata.io neurodata.io
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mindcontrol-hbn.herokuapp.com mindcontrol-hbn.herokuapp.com
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timvanmourik.github.io timvanmourik.github.io
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- Nov 2017
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ibg.colorado.edu ibg.colorado.edu
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- Oct 2017
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elifesciences.org elifesciences.org
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faseb.org faseb.org
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stolkarjen.github.io stolkarjen.github.io
- Sep 2017
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collaboration.humanbrainproject.eu collaboration.humanbrainproject.eu
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www.reproducibleimaging.org www.reproducibleimaging.org
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elifesciences.org elifesciences.org
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www.mcleanhospital.org www.mcleanhospital.org
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blogs.lse.ac.uk blogs.lse.ac.uk
- Aug 2017
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fairsharing.org fairsharing.org
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osf.io osf.io
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github.com github.com
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www.neurosciencenetwork.org www.neurosciencenetwork.org
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neuroscience.uchicago.edu neuroscience.uchicago.edu
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journals.plos.org journals.plos.org
- Jun 2017
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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The Experiment Factory: Standardizing Behavioral Experiments
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www.sjscience.org www.sjscience.org
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The Self-Journals of Science
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www.nature.com www.nature.com
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Finding useful data across multiple biomedical data repositories using DataMed
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ucsdnews.ucsd.edu ucsdnews.ucsd.edu
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NSF Awards $15 Million to Create Science Gateways Community Institute
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nsf.gov nsf.gov
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NSF commits $35 million to improve scientific software
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www.nature.com www.nature.com
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Extending transparency to code
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jea.acm.org jea.acm.orgACM JEA1
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RCR: Replicated Computational Results Initiaitve
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toms.acm.org toms.acm.orgACM TOMS1
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Replicated Computational Results (RCR)
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www.ieee.org www.ieee.org
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The Future of Research Curation and Research Reproducibility
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www.software.ac.uk www.software.ac.uk
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The Software Sustainability Institute
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science.sciencemag.org science.sciencemag.org
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Enhancing reproducibility for computational methods
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- May 2017
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www.nature.com www.nature.com
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Containerization technology takes the hassle out of setting up software and can boost the reproducibility of data-driven research.
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- Apr 2017
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openmediascholarship.org openmediascholarship.org
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- Mar 2017
- Feb 2017
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github.com github.com
- Jan 2017
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www.nature.com www.nature.com
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www.datacarpentry.org www.datacarpentry.org
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callingbullshit.org callingbullshit.org
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www.nature.com www.nature.com
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Replication studies offer much more than technical details
Another editorial highlighting that highlights the merits of replication beyond repeat and raises questions about the culture of science and confirmation bias.
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dev.openanatomy.org dev.openanatomy.org
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ohif.org ohif.org
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clowder.ncsa.illinois.edu clowder.ncsa.illinois.eduClowder1
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browndog.ncsa.illinois.edu browndog.ncsa.illinois.edu
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www.thelancet.com www.thelancet.com
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www.thelancet.com www.thelancet.com
- Dec 2016
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github.com github.com
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boutiques.github.io boutiques.github.io
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www.frontiersin.org www.frontiersin.org
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www.secretgeek.net www.secretgeek.net
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journal.frontiersin.org journal.frontiersin.org
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dmg.org dmg.org
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joss.theoj.org joss.theoj.org
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- Nov 2016
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guides.github.com guides.github.com
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What is GitHub?
Some pretty useful training material here.
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http://doi.org/10.5281/zenodo.61456
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www.w3.org www.w3.org
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Data on the Web Best Practices
A description for different qualities and targets for data sharing or publishing.
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samnicholls.net samnicholls.net
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Bioinformatics is a disorganised disaster and I am too. So I made a shell.
This is a shell-wrapper to minimize the effort needed to collect command line provenance.
This post covers a lot of ground to describe practical and human requirements.
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www.scientificpaperofthefuture.org www.scientificpaperofthefuture.org
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www.reproducibleimaging.org www.reproducibleimaging.org
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- In this paper, we have
Is something missing here?
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“Effect size and confidence interval”.
Hypothes.is has direct linking, so you could technically embed a link to the relevant section.
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github.com github.com
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science.sciencemag.org science.sciencemag.org
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repod.pon.edu.pl repod.pon.edu.pl
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- Oct 2016
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mindingthebrain.blogspot.com mindingthebrain.blogspot.com
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www.youtube.com www.youtube.com
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linkeddatabook.com linkeddatabook.com
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Linked Data: Evolving the Web into a Global Data Space
A comprehensive book on linked data.
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www.speirs.org www.speirs.org
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www.datacarpentry.org www.datacarpentry.org
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Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research.
Training for data skills
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www.wings-workflows.org www.wings-workflows.org
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WINGS is a semantic workflow system
A meta level representation of workflows.
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- Sep 2016
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hypothes.is hypothes.is
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clicking
clicking
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annotations
new
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www.pachyderm.io www.pachyderm.io
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A Containerized Data Lake
A data container + workflow spec
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hypothes.is hypothes.is
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Now you have the extension up
test
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camh-scwg.github.io camh-scwg.github.io
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camh-scwg.github.io camh-scwg.github.io
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Cool R tricks, Thanks, Erin!
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royalsocietypublishing.org royalsocietypublishing.org
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Natural Selection argument...
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neurohackweek.github.io neurohackweek.github.io
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www.nhlbi.nih.gov www.nhlbi.nih.gov
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events.brainhack.org events.brainhack.org
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2016 Brainhack LA
ReproNim co-sponsored event.
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neurohackweek.github.io neurohackweek.github.io
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Summer school
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www.bigdatau.org www.bigdatau.org
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The BD2K Guide to the Fundamentals of Data Science Series
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cryptogenomicon.org cryptogenomicon.org
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www.eur.nl www.eur.nl
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f1000research.com f1000research.com
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ReproNim
Neuroinformatics 2016 poster
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- Aug 2016
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neurohackweek.github.io neurohackweek.github.io
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Lesson template for Neurohackweek
A GitHub template for creating lesson plans. While this doesn't provide the flexibility of a computational environment within this lesson plan, it serves as a good approach to outline concepts of lessons.
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github.com github.com
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www.nature.com www.nature.com
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replication ecosystem, such as it is, lacks visibility, value and conventions.
a key social concern
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www.mkbergman.com www.mkbergman.com
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www.kaggle.com www.kaggle.com
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Welcome to Kaggle Datasets
Kaggle now allows publish datasets. It will be interesting to investigate what kind of datasets are allowed and how it captures metadata.
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projectreporter.nih.gov projectreporter.nih.gov
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Related to ReproNim TR&D2
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grants.nih.gov grants.nih.gov
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Metrics to Assess Value of Biomedical Digital Repositories
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bd2kccc.org bd2kccc.org
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BD2KCCC Webinars
BD2K Events that may be of general interest.
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www.frontiersin.org www.frontiersin.org
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Data Citation in Neuroimaging: Proposed Best Practices for Data Identification and Attribution
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www.futurelearn.com www.futurelearn.com
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journals.plos.org journals.plos.org
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The Virtuous Cycle of a Data Ecosystem
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waffle.io waffle.io
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Smart & Simple Project Management
another project management solution for GitHub and it appears to be free. i may replace zenhub with this.
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answers.semanticweb.com answers.semanticweb.com
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a very good first introduction to linked data / semantic web technologies with the "good and bad" ...
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www.statnews.com www.statnews.com
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Is this the sort of thing we want in ReproNIM?
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wibih.unomaha.edu wibih.unomaha.edu