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Rewarding Reproducibility and Method Publishing the GigaScience Way. Scott Edmu n ds GigaScience scott@gigasciencejournal.com @ gigascience / SCEdmunds. The Issue :. Data-driven science era brings: Huge opportunities Huge challenges with: data curation , review/QA, handling, sharing.

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rewarding reproducibility and method publishing the gigascience way

Rewarding Reproducibility and Method Publishing the GigaScience Way

Scott Edmunds

GigaScience

scott@gigasciencejournal.com

@gigascience/SCEdmunds

the issue
The Issue:
  • Data-driven science era brings:
  • Huge opportunities
  • Huge challenges with: data curation, review/QA, handling, sharing

= growing reproducibility gap

gigasolution deconstructing the paper
GigaSolution: deconstructing the paper
  • Take data publication approach further and reward:
  • Data availability
  • Metadata/curation
  • Interoperability
  • Availability of workflows
  • Transparent analyses

Analyses

Metadata

Methods

Data

gigasolution deconstructing the paper1
GigaSolution: deconstructing the paper

Combines and integrates:

Open-access journal

Data Publishing Platform

Data Analysis Platform

Utilizes big-data infrastructure and expertise from:

Worlds largest genomics organisation with: 17PB storage, 20.5K cores, 212TFlops, >1000 bioinformaticians

www.gigadb.org

www.gigasciencejournal.com

how are we supporting data reproducibility
How are we supporting data reproducibility?

Open-Data

Open-Paper

Data sets

DOI:10.5524/100038

Linked to

78GB CC0 data

DOI

Open-Pipelines

DOI

Open-Workflows

Linked to

DOI:10.1186/2047-217X-1-18

Analyses

DOI:10.5524/100044

>6500 accesses

Open-Review

8 reviewers tested data in ftp server & named reports published

Enabled code to being picked apart by bloggers in wiki

http://homolog.us/wiki/index.php?title=SOAPdenovo2

Open-Code

Code in sourceforge under GPLv3: http://soapdenovo2.sourceforge.net/

>4000 downloads

soapdenovo2 workflows implemented in
SOAPdenovo2 workflows implemented in

galaxy.cbiit.cuhk.edu.hk

soapdenovo2 workflows implemented in1
SOAPdenovo2 workflows implemented in

Implemented entire workflow in our Galaxy server, inc.:

  • 3 pre-processing steps
  • 4 SOAPdenovomodules
  • 1 post processing steps
  • Evaluation and visualization tools

Also available to download by >25K Galaxy users in

galaxy.cbiit.cuhk.edu.hk

slide9

“Deconstructed”

Journal

“Regular”

Journal

“Conscientious”

Online Journal

slide10

“Deconstructed”

Journal

“Regular”

Journal

“Conscientious”

Online Journal

slide11

“Deconstructed”

Journal

“Regular”

Journal

“Conscientious”

Online Journal

slide12

“Deconstructed”

Journal

“Regular”

Journal

“Conscientious”

Online Journal

Image Source: http://commons.wikimedia.org/wiki/File:System-Mechanic-California.jpg

slide13

Ultimate Goal: Executable papers

Data

Papers

Executable (Methods) Papers

Analysis

Papers

slide14

What is needed to make it happen?

Give us your data & pipelines!*

Contact us:

scott@gigasciencejournal.com

editorial@gigasciencejournal.com

database@gigasciencejournal.com

* APC’s currently generously covered by BGI

www.gigasciencejournal.com

slide15

Thanks to:

team:

Funding from:

Our collaborators:

Peter Li

Chris Hunter

Jesse Si Zhe

Nicole Nogoy

Tam Sneddon

Alexandra Basford

Laurie Goodman

RuibangLuo (BGI/HKU)

ShaoguangLiang (BGI-SZ)

Tin-Lap Lee (CUHK)

HuayenGao (CUHK)

QiongLuo (HKUST)

Senghong Wang (HKUST)

Yan Zhou (HKUST)

CBIIT

@gigascience

Follow us:

facebook.com/GigaScience

blogs.openaccesscentral.com/blogs/gigablog/

www.gigadb.org

galaxy.cbiit.cuhk.edu.hk

www.gigasciencejournal.com

slide16

Thanks to:

team:

Funding from:

Our collaborators:

Peter Li

Chris Hunter

Jesse Si Zhe

Nicole Nogoy

Tam Sneddon

Alexandra Basford

Laurie Goodman

RuibangLuo (BGI/HKU)

ShaoguangLiang (BGI-SZ)

Tin-Lap Lee (CUHK)

HuayenGao (CUHK)

QiongLuo (HKUST)

Senghong Wang (HKUST)

Yan Zhou (HKUST)

CBIIT

@gigascience

Follow us:

facebook.com/GigaScience

blogs.openaccesscentral.com/blogs/gigablog/

www.gigadb.org

galaxy.cbiit.cuhk.edu.hk

www.gigasciencejournal.com

Happy New Year!