Timestamp

6/4/15 17:18

Publication/preprint has complementing code & data repositories that can be used to reproduce results

10.7287/peerj.preprints.704 10.1101/012831

Code repositories have detailed, plain-English README files describing the computational environment and dependencies (including version numbers) to facilitate independent reproduction

https://github.com/jheare/OluridaSurvey2014 https://github.com/che625/olson-ms-nb https://github.com/sr320/eimd-sswd

Computational environment captured (ie. in a virtual machine image/dockerfile/vagrantfile, etc.) in one or more research compendia

na

Primary software tools for research are open source

IPython R IGV BSMAP BLAST Bedtools

Submit your code for review

Question not that clear, https://github.com/jheare/OluridaSurvey2014/issues/12

Perform code review for someone else

na

Have the substantive results of your publication reproduced by someone else using your code and data

Question not clear

Perform a reproducibility review for someone else

na

Analysis/scripts/code developed in one or more GitHub/BitBucket/GitLab or similar version-controlled open code repository

https://github.com/jheare/OluridaSurvey2014 https://github.com/che625/olson-ms-nb https://github.com/sr320/eimd-sswd

Code has one or more tests

na - and not clear what this means

One or more code repository has an open license (eg. MIT/BSD/GPL2 etc.)

na

One or more code repository has a persistent URL (eg. DOI) to a specific release

https://github.com/jheare/OluridaSurvey2014/releases/tag/v1.0 https://github.com/che625/olson-ms-nb/releases/tag/1.0

One or more datasets in an institutional repository (not personal webpage)

none

One or more datasets in Figshare/Zenodo or domain specific open data repository that issues persistent URLs

http://figshare.com/articles/Transcriptome_characterization_of_the_Olympia_oyster_and_pinto_abalone/156431 http://figshare.com/articles/QPX_Genome_Browser_Feature_Tracks/701214

One or more sets of raw data are published as soon as generated

tough question - maybe edit

One or more sets of raw data are in open formats (eg. CSV, txt, etc.)

maybe redundant? https://github.com/jheare/OluridaSurvey2014/tree/master/data

One or more Online Lab Notebooks

http://onsnetwork.org/halfshell http://figshare.com/articles/Lab_Notebook_2014/1273990

One or more grant proposals & data management plans online & Open Access

http://figshare.com/articles/DNA_methylation_as_a_mechanism_to_increase_adaptive_potential_in_invertebrates/97107 g https://github.com/sr320/LabDocs/blob/master/DMPseq.md https://github.com/sr320/LabDocs/blob/master/DataSharePlan.md

Preprint in arXiv, bioarXiv, PeerJ Preprints or similar

http://dx.doi.org/10.7287/peerj.preprints.704 http://dx.doi.org/10.1101/012831 http://figshare.com/articles/Genomic_resource_development_of_shellfish_of_conservation_concern/97205 http://figshare.com/articles/Elevated_pCO2_causes_developmental_delay_in_early_larval_Pacific_oysters,_Crassostrea_gigas/95828 https://peerj.com/preprints/388/

What percentage of your publications from the last two years are Open Access?

(not ness easy) 67%

Participation in open peer review via a Publons and/or PubPeer account or similar

https://publons.com/author/13038/steven-b-roberts#profile

Username

Your name and current affiliation

Steven Roberts, University of Washington, School of Aquatic and Fishery Sciences

An account at one or more web-based code-hosting service (eg. GitHub/BitBucket/GitLab or similar)