Before reproducibility must come preproducibility
This article touches on many components of the repronim project.
194 Matching Annotations
- May 2018
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www.nature.com www.nature.com
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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
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October 13-16, 2016
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2016 International Conference on Brain Informatics & Health
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events.brainhack.org events.brainhack.org
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Dates: September 18-20, 2016 Location: Vienna Austria Title: BrainHack Vienna
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- Jul 2016
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nautil.us nautil.us
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We Should Not Accept Scientific Results That Have Not Been Repeated
A nice article on reproducibility and need for structural change in science.
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journals.plos.org journals.plos.org
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Ten Simple Rules for Reproducible Computational Research
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force11.github.io force11.github.io
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Data Citations: A Primer
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wibih.unomaha.edu wibih.unomaha.edu
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2016 International Conference on Brain Informatics & Health October 13-16, 2016 in Omaha, Nebraska, USA
Date: October 13-16, 2016 Location: Omaha, Nebraska, USA
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identifiers.org identifiers.org
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Identifiers.org Identifiers.org is a system providing resolvable persistent URIs used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of a resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative.
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biosharing.org biosharing.org
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A curated, searchable portal of inter-related data standards, databases, and policies in the life, environmental and biomedical sciences
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www.w3.org www.w3.org
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Dataset Descriptions: HCLS Community Profile
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www.revolvy.com www.revolvy.com
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services.github.com services.github.com
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www.nationaldataservice.org www.nationaldataservice.org
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The NationalDATA SERVICE
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psycnet.apa.org psycnet.apa.org
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europepmc.org europepmc.org
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Sizing the Problem of Improving Discovery and Access to NIH-Funded Data: A Preliminary Study
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opendatabutton.org opendatabutton.org
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opennessinitiative.org opennessinitiative.org
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brainx.io brainx.io
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www.economist.com www.economist.com
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Might be good to have "fMRI in the news" section as well.
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ieeexplore.ieee.org ieeexplore.ieee.org
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datamed.org datamed.org
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blogs.warwick.ac.uk blogs.warwick.ac.uk
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Bibliometrics of Cluster Inference
ReproNIM should publish a set of guidelines for editors for evaluating and reporting resting state studies.
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learningequality.org learningequality.org
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An offline version of Khan Academy.
A lightweight deployable platform for teaching from khan academy.
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docs.google.com docs.google.com
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Spreadsheet of potential data resources for the Open Science Prize
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www.cambridgesemantics.com www.cambridgesemantics.com
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A beginner's introduction to Semantic Web and Linked Data.
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www.openscienceprize.org www.openscienceprize.org
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Open Science Prize
Initiative to promote and award open science
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Openness is a core value of scientific practice.
A set of badges to tag open science.
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try.github.io try.github.ioTry Git1
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Got 15 minutes and want to learn Git?
A tutorial from GitHub to learn git.
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates
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- Jun 2016
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aws.amazon.com aws.amazon.com
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github.com github.com
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cos.io cos.io
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www.biorxiv.org www.biorxiv.org
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www.nih.gov www.nih.govTraining1
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Training
NIH efforts towards reproducibility. This includes videos for training and discussion material as well.
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www.humanbrainmapping.org www.humanbrainmapping.org
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Open Science Special Interest Group
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github.com github.com
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open-brain-consent.readthedocs.org open-brain-consent.readthedocs.org
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www.openwebfoundation.org www.openwebfoundation.org
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contentmine.org contentmine.org
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www.scienceintheclassroom.org www.scienceintheclassroom.org
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centerforopenneuroscience.org centerforopenneuroscience.orgCON1
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dumontierlab.stanford.edu dumontierlab.stanford.edu
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reproducibility.stanford.edu reproducibility.stanford.edu
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Reproducibility matters
Stanford Center for Reproducible Neuroscience
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prakhar.me prakhar.me
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www.w3schools.com www.w3schools.com
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biocaddie.org biocaddie.org
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www.openaire.eu www.openaire.eu
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This is primarily for scholarly communication but also link to Zenodo for data I would tag with ReproNim:RelatedProject (in addition to current tags)
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singularity.lbl.gov singularity.lbl.gov
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An alternative to docker that Chris says is better for cluster and is designed for reproducibility
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www.codata.org www.codata.org
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DATA CITATION WORKSHOP: DEVELOPING POLICY AND PRACTICE
Title: DATA CITATION WORKSHOP: DEVELOPING POLICY AND PRACTICE Date: Tuesday, 12 July 2016 from 8:00 AM to 5:00 PM (EDT) Location: National Academies of Sciences, Engineering & Medicine - Keck Center, 500 Fifth St., NW, Room 100, Washington, DC, United States
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ckan.incf.org ckan.incf.org
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About
INCF DataSpace Powered by CKAN
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incf.github.io incf.github.io
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MINDS Schema
Minimal Information for Neuroscience Data Standard INCF - Dataspace effort
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datascience.nih.gov datascience.nih.gov
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The Commons supports biomedical discovery by enabling sharing of digital objects
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The open source data portal software
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www.humanconnectome.org www.humanconnectome.org
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Exploring the Human Connectome
Title: Exploring the Human Connectome Date: Aug 28-Sep1, 2016 Location: HMS, Boston, MA
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www.incf.org www.incf.org
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INCF Short course 2016
TItle: INCF Short course 2016 Dates: 31 August – 1 September, 2016 Location: Penta Hotel, Oxford Road, Reading RG1 7RH, United Kingdom
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python.g-node.org python.g-node.org
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Advanced Scientific Programming in Python
Title: Advanced Scientific Programming in Python Dates: September 5—11, 2016. Location: Reading, UK
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www.eventbrite.com www.eventbrite.com
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THOR Workshop
Date: July 7, 2016 Location: Amsterdam, Netherlands Type: Workshop
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datascience.nih.gov datascience.nih.gov
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Title: Wold-Scale Personalized Learning through Crowdsourcing and Algorithms
Date: June 1, 2016 Time: 3:30pm - 4:30pm EST
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arxiv.org arxiv.org
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THE NATURAL SELECTION OF BAD SCIENCE
Do we want to have a bibliography associated with ReproNIM?
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www.youtube.com www.youtube.com
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clearly for introduction, lasts 15 min, very clear, would be great to have a couple of exercices to accompany the video
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- May 2016
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www.pgbovine.net www.pgbovine.net
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vida-nyu.github.io vida-nyu.github.io
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www.nomadproject.io www.nomadproject.io
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Easily deploy applications at any scale
A modern distributed scheduler
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americanbiomedicalinformatics.org americanbiomedicalinformatics.org
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Graph Based Analysis of Biomedical BigData
Title: Graph Based Analysis of Biomedical BigData Date: Thursday July 7 - Friday July 8, 2016 Location: University of District of Columbia CC, Washington DC Type: 2 Day Hands-on Training
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