Supplementary Table 1: Sharing Initiatives

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Oct 21, 2013 (3 years and 7 months ago)

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Supplementary Table 1: Sharing Initiatives

Project name

Sharing functionality

Sharing trends

Commercial



DNAnexus

http://sra.dnanexus.com/

Hosts

National Center for
Biotechnology Information
(NCBI) Sequence Read

Archive

(SRA) for raw
sequence data from next
-
gen
sequencing platforms.

Built user interface and mirrors 300
-
400
terabytes of SRA data (no medical data) on
Google’s cloud.
Offers proprietary cloud
-
based
analysis and visualization tools that users can
sha
re.


Illumina

https://basespace.illumina.com/home


Data
-
sharing, analysis and
storage for Illumina platform
users

BaseSpace, genomics d
ata
-
sharing space on
Amazon’s AWS cloud infrastructure, in beta
t
esting phase. Requires user registration.

Life

T
echnologies

Ion Torrent
Community

http://www.iontorrent.com/communit
y/

User portal share data,
protocols and code

Sharing portal Ion
Torrent
Community requires
user registration

Complete Genomics

http://
www.completegenomics.com/s
ervices/data
-
management
-
analysis/


Offers sequencing services,
data management, analysis,
and
results
sharing.

Downstream analysis and data sharing services
invade market of software service providers.

Genedata

http://www.gened
ata.com/profession
al
-
service/data
-
analysis.html

S
oftware has built
-
in sharing
f
unctionality for power
-
users
and workflow users

Positioned for pharma outsourcing and public
-
private projects, such as Europe’s
InnoMedPredTox.

http://www.imi.europa.eu/content/pilot
-
project
-
innomed

GenomeQuest

http://www.genomequest.com/techno
logy

Sharing functionality built
into analysis tools

As cust
omer sharing behavior changes,
less
interest in data s
torage. More sharing of analysis
results that sharing of raw data.

ID Business Solutions

http://www.idbs.com/products
-
and
-
services/inforsense
-
suite/

Software and consulting firm
with platform for data
analysis and data integration,
InforSense Suite

Lu
ng Genomics Research Consortium expanded
one of suite’s components, ClinicalSense, for its
data analysis and sharing portal

Non
-
commercial allian
c
es

Description

Projects

Pistoia Alliance

http://www.pistoiaalliance.org/

Collaborative group of
pharma and
life sciences
companies exploring pre
-
competitive data
-
sharing.



Launches data
-
sharing projects for next
-
gen
sequence data, biomarker exchange standards.
R
uns competitions, for ex. Sequence Squeeze
Competition seeking algorithm to compress
next
-
gen sequ
ence data

BioIT Alliance

http://bioitalliance.org/

F
ounded by Microsoft, now a
non
-
profit organization.


Seeks to create standards

data models and
transmission standards

to enable data
-
sharing
in translational medicine

Non
-
profit
init
i
atives



BioSh
aring

http://
Biosharing.org

International network of
organizations geared toward
data
-
sharing and
standardization in the life
sciences

Developed standard called ISA Commons to
streamline data sharing

crowdLabs

http://www.crowdlabs.org/


Repository for c
omputational
workflows
(not only life
sciences); offers
acces
s to
high performance computing

Uses VisTrails, an open source workflow
system.


Galaxy

http://galaxy.psu.edu/



Web and cloud
-
based open
source sequence
analysis
tools

Galaxy Pages lets users see, re
-
use, and extend
workflows

http://wiki.g2.bx.psu.edu/Learn/Galaxy%20Page
s

myExperiment Virtual Research
Collaboration between the
Platform to share workflows. Users can share
Environment

http://www.myexperiment.org/

universities of
Southampton
,
Manchester

and
Oxford

in
the UK.

workflows openly or

keep them private.

National Center for Biotechnology
Information (NCBI)

http://www.ncbi.nlm.nih.gov

Online resources with
databases and analysis tools.
A division of the National
Library of Medicine at the
National Institutes of Health.

DNA sequence r
esource, GenBank, run by NIA,
EMBL and DNA DataBank of Japan. Dozens of
terabytes of data are downloaded from NCBI
resources every day.

Sage Bionetworks

http://sagebase.org/

A non
-
profit focused on
sharing science founded by
former Merck researchers
Step
hen Friend and Eric
Schadt

Launches research collaborations, for example
the public
-
private CommonMind Consortium to
share neuropsychiatric disease

World Wide Web Consortium
Semantic Web

http://www.w3.org/2001/sw/

Part of the international
community orga
nization
World Wide Web
Constorium (W3C)

Has groups devoted to data
-
sharing in the life
sciences, for example Semantic Web Health
Care and Life Sciences Interest Group

Workflow 4 Ever

http://ww
w.wf4ever
-
project.org/web/guest/home

Web
-
based resource to
preserve and share methods
and workflows.

Has partners in genomics and astronomy.
Complementary to SHIWA (Sharing
Interoperable Workflows for large
-
scale
scientific simulations on distributed comp
uting
infrastructures)

Sharing networks and repositories



BioPortal

http://bioportal.bioontology.org/

R
epository run by The
National Center for
Biomedical Ontology, part of
the
National Centers for
Biomedical Comp
uting


Has portal stores over 300 controlled
vocabularies and ontologies in biomedicine.
Users can submit download ontologies and
upload them to share with others.

Concept Web Alliance
http://www.nbic.nl/about
-
nbic/affiliated
-
organisations/cwa/introduc
tion/

Group effort addressing
s
emantic web applications,
based at The Netherlands
Bioinformatics Centre

Establishing uniform, user
-
friendly online
platform for text
-
mining from published texts,
databases, and offline resources.

Cytoscape

http://www.cytos
cape.org/

Open
-
source software to
analyze and visualize
biological networks

Developers are working on a database for
sharing network models.

Datacite

http://datacite.org/

A non
-
profit, international
organization of libraries

Offers service for data publ
ishers to mint Digital
Object Identifiers (DOIs) for data
-
sharing. DOIs
are also available for datasets. Datacite is
compiling a list of research data repositories and
working on ways to use DOI to retrieve
metadata.

Force11

http://force11.org/

A group
of editors,
publishers, scientists
librarians, and research
funders

Formed
in 2011 to explore new ways to share,
create, and communicate scholarly knowledge.

Genocoding Project

http://text.soe.ucsc.edu/

A

data harvesting initiative
based at the universit
y of
California at Santa Cruz and
the University of Manchester

Software tool scans
journal papers for genomic
identifiers and maps them to human genome.

Nanopublications
http://
www.nanopub.org

A venture seeking to

use
semantic tools to harvest
assertions and to them with
DOIs

Nanopublications are being tested in Open
Pharmacological Concepts Triple Store (Open
PHACTS), a European public
-

private venture
http://www.openphact
s.org

EMBL: European Molecular Biology Laboratories.
Sources:
Nature Biotechnology

research, Frost &
Sullivan, company data