While we can certainly improve on our efforts to make our work open and reproducible, we have published a series of products over the last few years that have had associated code/data repositories that have accompanied the narratives (aka manuscripts). I will try to recap said efforts here as a means to show others different options, as well as point out ways we can improve going forward.

Case 1

Gavery MR, Roberts SB. (2013) Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc. PeerJ 1:e215 https://dx.doi.org/10.7717/peerj.215

This was one of our early efforts where we provided the ability to view genomic feature tracks in Integrative Genomics Viewer and the SQLShare query used to derive the methylation feature track from the original methratio output.

Predominant_intragenic_methylation_is_associated_with_gene_expression_characteristics_in_a_bivalve_mollusc__PeerJ__1BBEED09.png

pic http://figshare.com/articles/Crassostrea_gigas_high_throughput_bisulfite_sequencing_gill_tissue_/749728

We also linked out to a webpage with more instructions http://oystergen.es/bigill

Case 2

Garcia-Vedrenne AE, Groner M, Page-Karjian A, Siegmund G-F, Singhal S, Sziklay J and Roberts SB. (2013) Development of Genomic Resources for a thraustochytrid Pathogen and Investigation of Temperature Influences on Gene Expression PLoS ONE 8(9): e74196. doi:10.1371/journal.pone.0074196

In this particular case we cited the figshare repository in the paper itself.

PLOS_ONE__Development_of_Genomic_Resources_for_a_thraustochytrid_Pathogen_and_Investigation_of_Temperature_Influences_on_Gene_Expression_1BBEEEB4.png

qpx http://figshare.com/articles/QPX_Genome_Browser_Feature_Tracks/701214

Case 3

Olson CE and Roberts SB. (2014). Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes Frontiers in Physiology. 5:224. doi: 10.3389/fphys.2014.0022

This is an edge case where figshare was used for supplemental analysis, though a tiny bit of R code is part of the repo.

Frontiers___Genome-wide_profiling_of_DNA_methylation_and_gene_expression_in_Crassostrea_gigas_male_gametes___Invertebrate_Physiology_1BBEF472.png

olson http://figshare.com/articles/Crassostrea_gigas_male_gonad_transcriptional_data_comparison/1004464

Case 4

Timmins-Schiffman E, Coffey WD, Hua W, Nunn BL, Dickinson GH and Roberts SB. (2014). Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas BMC Genomics 2014, 15:951 doi:10.1186/1471-2164-15-951

With this paper we added data to a PANAGAEA for the first time per request. The citations to figshare doubled here (2), where one is a simply a PDF that (in theory) could be used to reproduce the proteomics data results in SQLShare. This is complex as it is a combination of links and SQL commands. A unique problem here is that SQLShare is moving servers, so this breaks. The second figshare citation is the full size pathway analalysis figures that allow people to interact with the data better. This paper is prime for some form of interactiveness.

BMC_Genomics___Full_text___Shotgun_proteomics_reveals_physiological_response_to_ocean_acidification_in_Crassostrea_gigas_1BBEF69E.png

pan http://doi.pangaea.de/10.1594/PANGAEA.837671

BMC_Genomics___Full_text___Shotgun_proteomics_reveals_physiological_response_to_ocean_acidification_in_Crassostrea_gigas_1BBEF5D2.png

SQLShare_workflow_for_proteomics_analysis_1BBEF64E.png
http://figshare.com/articles/SQLShare_workflow_for_proteomics_analysis/894323

iPath2_supplemental_information_1BBEF672.png
http://figshare.com/articles/iPath2_supplemental_information/899908

Case 5

Fuess LE, Eisenlord ME, Closek CJ, Tracy AM, Mauntz R, Gignoux-Wolfsohn S, Moritsch MM, Yoshioka R, Burge CA, Harvell CD, Friedman CS, Hewson I, Hershberger PK, Roberts SB (2015) Up in Arms: Immune and Nervous System Response To Sea Star Wasting Disease PLoS ONE doi:10.1371/journal.pone.0133053

Here is where things start getting a little better…

PLOS_ONE__Up_in_Arms__Immune_and_Nervous_System_Response_to_Sea_Star_Wasting_Disease_1BBEF736.png

PLOS_ONE__Up_in_Arms__Immune_and_Nervous_System_Response_to_Sea_Star_Wasting_Disease_1BBEF78F.png

eimd-sswd_v1_0__Supplemental_Jupyter_notebooks_and_data_1BBEF7FB.png
http://figshare.com/articles/eimd_sswd_v1_0_Supplemental_Jupyter_notebooks_and_data/1441384

sr320_eimd-sswd_1BBEF81A.png
https://github.com/sr320/eimd-sswd

Case 6

Heare JE, Blake B, Davis JP, Vadopalas B, Roberts SB. (2014) Evidence of Ostrea lurida (Carpenter 1894) population structure in Puget Sound, WA. PeerJ PrePrints 2:e704v1 http://dx.doi.org/10.7287/peerj.preprints.704

Now we are into “preprints” (and we will continue to be into them). For this particular paper, data was analyzed with R, using a GitHub repo, and doi’d with Zenodo.

Evidence_of_Ostrea_lurida__Carpenter_1864__population_structure_in_Puget_Sound__WA__PeerJ_PrePrints__1BC01888.png

OluridaSurvey2014__JSR_-_Zenodo_1BC01903.png
https://zenodo.org/record/30373

jheare_OluridaSurvey2014_1BC01964.png https://github.com/jheare/OluridaSurvey2014

This link with Zenodo is nice. Every time you create another release, Zenodo automatically updates.

Case 7

Claire E. Olson, Steven B. Roberts. Indication of family-specific DNA methylation patterns in developing oysters bioRxiv doi: http://dx.doi.org/10.1101/012831

Another preprint, this time on bioRxiv. This is probably our most reproducible work. It is done in a Jupyter notebook (fomerly IPython). In the paper the Github is directly cited.

biorxiv_org_content_biorxiv_early_2015_03_13_012831_full_pdf_1BC01AE5.png

che625_olson-ms-nb_1BC01A88.png https://github.com/che625/olson-ms-nb

Case 8

Influence of 17α-ethinylestradiol on DNA Methylation in Oysters paper-Oyster-EE2: v1.5. Zenodo. 0.5281/zenodo.19046 https://github.com/sr320/paper-Oyster-EE2/blob/master/Gavery-Roberts-EE2.md

This is the most different. The entire work is on GitHub, doi’d with Zenodo.

sr320_paper-Oyster-EE2_1BC01BD3.png https://github.com/sr320/paper-Oyster-EE2

sr320_paper-Oyster-EE2_1BC01C04.png

Case 9

Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change- Draft @ https://www.authorea.com/users/16716/articles/18248/_show_article

This paper has a robust repo, it includes both Jupyter notebooks and R code. Also this is the first time we have used Authorea to draft the paper. It has been submitted and accepted in Molecular Ecology.

jldimond_Coral-CpG_1BC01D59.png https://github.com/jldimond/Coral-CpG

9 Ways to Make Papers a Little More Open and Reproducible
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