The overall component of our 2016 RPPR annual report for NRNB

1. NRNB
Annual
Report
2016
-­‐-­‐
Overall
B.1:
Specific
aims
The mission of the National Resource for Network Biology is to advance the science of
Biological Networks by providing leading-edge bioinformatic methods, software and
infrastructure, and by engaging the scientific community in a portfolio of collaboration
and training opportunities. Biomedical research is increasingly dependent on knowledge
of biological networks of multiple types and scales, including gene, protein and drug
interactions, cell-cell and cell-host communication, and vast social networks. NRNB
technologies enable researchers to assemble and analyze these networks and to use
them to better understand biological systems and, in particular, how they fail in disease.
NRNB has been funded as an NIGMS Biomedical Technology Research Resource since
2010.
Our overall mission is accomplished through the following five Specific Aims:
Specific Aim 1. To mount aggressive programs of research in cutting-edge
bioinformatic technology to address major challenges and opportunities in Network
Biology. In past years, we introduced a series of innovative methods including network-
based biomarkers and network-based stratification of genomes. In the next support
period, we will research approaches to represent and analyze network architecture
across conditions or times; a general engine for genotype-to-phenotype prediction using
network knowledge; and a platform to crowd-source construction of a gene ontology
based wholly on network data from the community. Research proceeds in frequent
communication with Driving Biomedical Projects, which provide data and applications
from the labs of our close collaborators.
Specific Aim 2. To catalyze phase transitions in how biological networks are
represented and used in biomedical research. We are well-positioned to catalyze
change along three complementary themes: I. Moving from static network data and
models to networks that are differential or dynamic, II. Moving from networks that are
primarily descriptive to those that are predictive of a range of phenotypes and behaviors,
and III. Moving from flat networks (lists of pairwise interactions) to multi- scale
representations that capture the hierarchy of modules comprising a biological system
and reflected in its data.
Specific Aim 3. To establish and disseminate robust end-user software, databases and
high- performance computing infrastructure that enable network analysis and
visualization methods for a broad biomedical research community. We will further
develop the popular Cytoscape desktop application and App Store database of network
analysis tools into a mature platform for network-based research on the web and in the
cloud, to be called the Cytoscape Cyberinfrastructure. We will grow the collection of
supported network tools distributed through nrnb.org. And we will update and expand the
current NRNB computing hardware to keep pace with the growing size of network
datasets and computing tasks.
Specific Aim 4. To engage with leading biomedical investigators in productive
collaborations

2. uniquely enabled by NRNB methods and tools. Since our inception in 2010, the NRNB
has maintained an active and rolling portfolio of approximately 60-80 Collaborative and
Service Projects. We will use best practices learned during this initial period of support to
continue to acquire, triage, and/or complete collaborative projects, with an increasing
focus on deploying new network methodologies developed under the three major
technology themes outlined in Aim 2.
Specific Aim 5. To train the current and next-generation of biomedical investigators in
the science of Network Biology and its applications in disease research. The NRNB runs
a highly attended annual network biology symposium, which starting in 2014 is planned
jointly with DREAM and ICSB/RECOMB. We run a broad collection of network biology
workshops and training events, including a very popular Google Summer Of Code
program which over the past 4 years has recruited over 50 mentors and 100 students
around the world to work on network biology projects under matching support from
Google.
B.2:
What
was
accomplished
Highlights
from
the
past
year
include:
• 103 publications citing NRNB grant
• 800 citations of Cytoscape publications
• 100s of users and dozens of developers trained on Cytoscape by NRNB staff
• 428 members in our Network Biology LinkedIn group
• 1750 members and 4200 messages on our two Google groups for Cytoscape
• 9000 visits per week to Cytoscape.org
• 14,000 downloads per month for Cytoscape
• 3700 Cytoscape application launches per day
• 42,000 page views in January 2016 for the Cytoscape App Store, and 580
downloads per day
• The top 4 of 5 Google search results for "network biology tools" are all NRNB site
pages. It is even in the top 10 results (#6 today) when searching for just "network
biology". These are global, non-personalized results.
• A total of 17 tools supported by NRNB
• 48 active and pending collaborations with external investigators on diverse topics
• 5 students trained at NRNB Academy last year
• 20 NRNB coordinated training events in 6 countries
• 71,000 unique sessions at Open Tutorials, 60% from new visitors
• 26 open access Cytoscape app articles edited for F1000Research channel
Technology
Research
and
Development
We launched three themes of technology research and development in our first year of
renewed support for the NRNB. Progress on the first theme of Differential Networks
includes work on optimization of network inference parameters for more accurate
models of perturbations (i.e., high-throughput drug response data) of biological systems.
We performed drug-target network analysis in our DBP 7 to identify upregulated targets
in liposarcoma cell lines in response to a CDK4 inhibitor. We also continued to develop
protein-protein interaction network alignment algorithms. And we implemented new tools
in Cytoscape for working with mass spec data to facilitate future differential network

3. analysis. This work was shared with our DBP 1, the Krogan lab, from which we continue
to collect valuable end-user input to design and prioritize our tool development.
The second theme of Descriptive to Predictive Networks saw progress on two specific
sub-aims. We developed a new machine learning method that uses patient similarity
networks as features to predict disease outcome and successfully applied it to the
prediction of Autism Spectrum Disorder phenotype from germ line DNA. We also
continued to refine our network-based stratification approach to classifying subtypes of
cancers, applying it most recently to newly available data from the Pan-Cancer Analysis
of Whole Genomes. The next steps in this projects, as described in B.6, will provide a
new resource for network analysis of drug response as proposed by Pommier, DBP 8.
Progress on the third theme of Multi-scale Networks includes the development of a
general progressive procedure, Active Interaction Mapping, which was used to assemble
a comprehensive ontology of functions for autophagy. This work continues to be
motivated by the data and prediction challenges in DBP 3 and 4, Mike Cherry (GO) and
TCGA projects. We have also begun experimenting with using single cell RNA-seq data
to improve the resolution of inferred cell-cell interaction networks. These are being
applied to cancer stem cell biology and regenerative medicine. This work is being driven
by Dr. Zandstra’s sustained interest in both inter-cellular networks and cell fate
regulation, DBP 9.
Collaboration
and
Service
Projects
NRNB staff have initiated 48 collaboration and service projects over the reporting period.
A summary table is provided in the CSP component report, along with summaries of
major project from each of the four sites led by the co-PIs. In broad strokes, the projects
span online integration of network technology and knowledge bases, development of
Cytoscape apps and cytoscape.js enhancements, co-author networks in drug
development, customized one-on-one training sessions, and pathway and network
analysis of hematopoietic and leukemic stem cells, AML, IL-7 pathways, lipid signaling,
gliobastoma, musculoskeletal tumors, ophthalmopathy, HIV, breast cancer, head and
neck cancer, ovarian cancer, and prostate cancer.
Infrastructure
We have created the initial technologies needed to create an ecosystem of biologically
valuable Internet-based services that exchange network data in a stable, performant,
scalable, reusable, recombinable, and reliable manner. These include the CX network
transfer format, CyWidgets of encapsulated web application library code, and a scalable
service router called Elsa.
During this period we have launched our Future of Publishing initiative, which envisions
web-based journal publishers to make dynamic content available with their articles. As a
pilot, Elsevier has leveraged the web-based cytoscape.js rendering library to add
interactive networks to their ScienceDirect articles when authors supply Cytoscape
network files (e.g., http://www.sciencedirect.com/science/article/pii/S2352340915000724).
Since March 2014, we have built the NRNB Cluster, deployed eight high throughput
computational workstations, laptops and desktop PCs, and deployed a VMware server
farm. Papers resulting from cluster usage are listed in section B.5 of the Infrastructure
report. Over the last year, 90% of the NRNB cluster nodes have been saturated with
NRNB-sponsored jobs 90% of the time.

4. Dissemination
NRNB.org is the main web site for the National Resource for Network Biology and
serves as the primary source of disseminating NRNB resources and associated
information. It is constantly updated with information for NRNB collaborators and
researchers as well as the larger network biology community. The site includes our
project description and annual reports, available tools and resources, links to training
materials, programs and events, and instruction in how to collaborate. The attentive
maintenance and updating of the site helps make the top 4 of 5 Google search results
for "network biology tools" all NRNB site pages. It is even in the top 10 results (#6 today)
when searching for just "network biology". These are global, non-personalized results.
Over the past year, traffic to the site averages about 850 visits per month. Since the site
went live in late 2010, we have had over 73,000 visits.
Since our last report (March 2014), we significantly reorganized the look of the
cytoscape.org web site, added new pages to support users and developers, and
upgraded the Download page to streamline the Cytoscape download process. We also
added pages to advertise available Cytoscape-related jobs, a development vision and
roadmap, statistics on many facets of Cytoscape usage, and a new Troubleshooting
page. Statistics on Cytoscape downloads by version, Cytoscape.org visits, launches of
Cytoscape sessions by users, and citations of Cytoscape and associated funding
agencies are all provided in the Dissemination report.
During this period, the Cytoscape App Store, which was created as an NRNB
supplement project, continues to serve as the major source of dissemination for
Cytoscape apps and related documentation. The App Store hosts over 260 apps
developed by 588 different developers around the world. Cytoscape users download an
average of 580 apps per day over the past 12 months. That has accumulated to just
over 400,000 app downloads. During the month of January 2016, the site received over
42,000 page views. Graphs of app submissions, site visits and referral sources are all
provided in the Dissemination report.
NRNB staff members are responsible for maintaining these additional sources of
dissemination:
• Three Cytoscape mailing lists: helpdesk, discuss and cytostaff
• Cytoscape competitions: http://nrnb.org/competition-2016.html
• Open Tutorials: http://opentutorials.cgl.ucsf.edu/index.php/Main_Page
• Cytoscape Publications Tumblr: http://cytoscape-publications.tumblr.com/
• Network Biology Publications Tumblr: http://netbiopub.tumblr.com/
• LinkedIn Network Biology Group: https://www.linkedin.com/groups/5123610
• F1000Research Cytoscape App Channel:
http://f1000research.com/channels/cytoscapeapps
• NRNB Academy SS 2015: http://www.nrnb.org/gsoc.html
Training
The Training Coordinator, Dr. Morris, conducts the majority of training events for NRNB
tool users and potential developers. We also leverage the fact that we are a multi-site
resource and are thus able to host local training events on 4 different campuses. We
also provide materials, training and advertising for events presented by non-NRNB staff.
The Training report includes a table of 20 events coordinated by the NRNB, including
courses, workshops, clubs and lectures in 6 countries.

5. New in this proposal, is an effort to train and consult for Bioinformatics Core personnel at
research institutions to leverage their unique positions interfacing with a broad, ever-
changing set of research projects. We are piloting this effort locally at UCSD and
Gladstone Institutes via Drs. Ideker and Pico, respectively.
For the first time since establishing NRNB Academy, we ran a special Summer Session
in 2015 where we successfully mentored 4 students, out of a pool of 13 applicants. Our
2015 end-of-year report for NRNB Academy Summer Session can be found here:
http://nrnb.org/gsoc-reports.html. We have received and abundance of testimonials from
students and mentors, a subset of which are available on our website:
http://nrnb.org/testimonials.html#collab-tab.
B.4:
What
training
opportunities
Our collaboration and service projects during this period included many requests to
prepare a custom training events and one-on-one sessions (see Services in CSP report
B.2. table). For example, a small workshop for performing network visualization and
analysis of mass spec data in Cytoscape was prepared by Drs. Morris and Pico. The
Bader group also offered support to local researchers by consulting meetings and one-
on-one training sessions.
Our Training effort leveraged the fact that we are a multi-site resource and are thus able
to host local training events on 4 different campuses. We also provided materials,
training and advertising for events presented by non-NRNB staff. The Training report
includes a table of 20 events coordinated by the NRNB, including courses, workshops,
clubs and lectures in 6 countries.
B.5:
How
have
results
been
disseminated
Technology
Research
and
Development
Technology research and development results are routinely published (see C.1) and
discrete software tools and resources are highlighted and distributed through the NRNB
web site at http://www.nrnb.org/tools-wall.html.
Infrastructure
We routinely promote Cytoscape and other NRNB infrastructure advancements through
publications and via the tools page on the nrnb.org web site. Publications citing
Cytoscape continue to increase year over year, numbering 799 in 2015, a 14% increase
over 2014. NRNB staff were involved in at least 15 publications using Cytoscape and
results obtained on the NRNB cluster. These are listed in the Infrastructure report.
Training
All of the activities reported in the Training component are providing “training
opportunities.” These are opportunities that in most cases would not exist without NRNB
staff and support. Each year we provide 100’s of researchers an introduction to network
biology concepts and Cytoscape usage. We also train dozens of programmers how to

6. write apps for Cytoscape to provide domain-specific functionality to the platform. These
programs have been very successful so far. This is evident from the testimonials we
collect via survey following each event: http://nrnb.org/testimonials.html#collab-tab.
B.6:
What
you
plan
to
do
next
Technology
Research
and
Development
For the first theme of Differential Networks, we plan to undertake a comprehensive data
mining effort to inform the parameterization of prior confidence scores to further improve
the network inference scheme described in B.2 and the original grant research strategy.
The network alignment work will take into account the evolution of domain and binding
site changes. And we will continue to tackle the long list of improvements to Cytoscape
prioritized for mass spec practitioners and use cases, such as semi-automated identifier
mapping and a API for running external jobs from within Cytoscape.
Work on the second theme of Descriptive to Predictive Networks will progress during
the next period via the continued development of a comprehensive pathway enrichment
analysis workflow in Cytoscape, linking to GeneMANIA. In the area of subtype
classification based on networks, we consider the impact of integrating both coding and
non-coding mutations versus coding alone, as well as network structure modifications,
e.g., due to mutations in TF binding sites. Extending molecular network knowledge to
include not only gene and protein interactions but also interactions involving regulatory
elements, will provide a new resource for network analysis of drug responses.
The third theme of Multi-scale Networks will see the application of our data-driven
ontology construction methods to human biology and investigations into the
mathematical functions that integrate information across the many layers of hierarchy
from genotype to phenotype. We will also plan to continue to make improvements in the
inference cell-cell interaction networks by including cell receptor-ligand interactions, and
applying this technology to cancer stem cell biology and regenerative medicine.
Collaboration
and
Service
Projects
New CSP requests are coming in all the time. We will continue to evaluate these per site
as we have. New to this renewal, however, is the approach being tested by Gladstone
and UCSD sites to have their respective Bioinformatics core facilities explicitly offer
NRNB services as part of their regularly advertised campus services. Both groups have
already seen many projects funnel in through this mechanism. We will continue to
evaluate this approach and scale it where appropriate. See the CSP report for a more
detailed description of specific projects on the horizon at each site.
Infrastructure
The overall goals for the Cytoscape Desktop are published on the Cytoscape Roadmap
web page (http://cytoscape.org/roadmap.html). The Infrastructure report summarizes
these and goes into detail on future Cytoscape Cyberinfrastructure and NRNB Cluster
work plans.
We also plan to adapt the Cytoscape App Store over the next reporting period to enable
support for the Cytoscape Cyberinfrastructure (CI). Through the CI Store, application

7. programmers will be able to discover the existence, purpose, documentation, and API
interface for services available for either immediate use or installation on private servers.
Training
New training materials, continued stream of training events and an upgraded GSoC
effort are in the works for the next reporting period. We were just recently notified that
we have been accepted to present an Introduction to Cytoscape workshop at the
upcoming ISMB meeting in Orlando, Florida. This is a major conference in bioinformatics
and systems biology. The conference includes the Network Biology community of
special interest (COSI), which we started as NRNB representatives 5 years ago. We
expect a good turn out for this training event, with a high rate of adoption and follow-up
activity. So, for the next reporting period, we plan to overhaul our Introduction to
Cytoscape materials and make some critical improvements.
We also just recently submitted our application for GSoC 2016. If accepted, this should
be one of our largest years yet. We have more mentors and more project ideas than
prior years and are organizing a more coordinated outreach effort with a Student
Outreach Packet that we will distribute to all NRNB mentors to help them contact and
communicate with various student bodies that are likely to have the skill and interest to
participate in GSoC 2016.
C.2:
Website(s)
or
other
internet
site(s)
NRNB.org
NRNB.org is the main web site for the National Resource for Network Biology and
serves as the primary source of disseminating NRNB resources and associated
information. It has information for NRNB collaborators and researchers as well as the
larger network biology community. The site includes our project description and annual
reports, available tools and resources, links to training materials, programs and events,
and instruction in how to collaborate. Over the past year, traffic to the site averages
about 850 visits per month. Since the site went live in late 2010, we have had over
73,000 visits.
Cytoscape.org
As detailed in the Dissemination report, cytoscape.org has been significantly
reorganized since our last progress report. New jobs, roadmap and usage content has
been added to the site, as well as upgrades to the troubleshooting and download pages.
As measured by Google Analytics, visits to the cytoscape.org web site have increased
markedly year over year. Visits to cytoscape.org now number almost 1.5M since the site
was created in 2012. And Cytoscape is being started approximately 3,500 times during
weekdays throughout the world, and over 1,000 times during the weekends and
holidays. This is nearly double the volume measured in 2014. Finally, the frequency of
which Cytoscape is cited in papers indexed in PubMed continues to increase year over
year, as shown below. The citation rate increase between 2014 and 2015 is 14%.

8.
Cytoscape
App
Store
A highlight of NRNB Dissemination efforts is the Cytoscape App Store
(http://apps.cytoscape.org/), which was developed under supplemental funding to the
main NRNB award. The goals of the App Store are to highlight the important features
that apps add to Cytoscape, to enable researchers to find and install apps they need,
and for developers to promote their apps. It has stimulated a sizable community of
Cytoscape App developers, hosting over 260 apps developed by 588 different
developers around the world. Cytoscape users download an average of 580 apps per
day over the past 12 months. That has accumulated to just over 400,000 app
downloads. The average submission rate remains between 2 and 3 new apps per
month. During the month of January 2016, the site received over 42,000 page views. As
shown below, there have been 335,340 visits since the store was staged in mid 2012 –
an average of 11 visitors per hour, with year-over-year visits continuing to increase.
Associated graphs are available in the Dissemination report.
OpenTutorials
Open Tutorials (http://opentutorials.cgl.ucsf.edu/index.php/Main_Page) is the main
source for tutorial materials for Cytoscape and other NRNB tools, and is being used both
internally by presenters, and by researchers and developers. The site now hosts 6
detailed user tutorials and 3 developer tutorials. Traffic to Open Tutorials is consistent,
with over 71,000 unique sessions in the last year, a slight increase over the previous
year.
Others
As detailed in Administrative, Dissemination and Training reports, we also maintain a
handful of other sites related to NRNB activities, including
• Network Biology LinkedIn group
• Tumblr feeds for Network Biology- and Cytoscape-related publications
• Special pages for GSoC and NRNB Academy
• Special pages for annual NetBio SIG conference
• Cytoscape competition events and results
• Guest editor roles for F1000Research Channel for Cytoscape Apps
• New Cytoscape App Developer Ladder
• New site for hosting a dynamically generated manual for Cytoscape
C.3:
New
technologies
and
techniques
TRD
1.1
The discussed improvement to the perturbation biology methodology is a significant
technology that has been publicly shared via publication. Additionally, there is an
accompanying web application (http://www.sanderlab.org/pertbio/) that is available.
Users can explore the data from the analysis and download models produced by the
analysis.

9.
TRD
1.2
As mentioned in sections B.2 and B.6, our major new technologies are progressing in all
three TRDs. We are particularly excited about our precision medicine patient network
results which we hope will translate into applications in a wider set of diseases in 2016.
TRD
1.3
The new network import dialog as described and pictured in B.2. is being shared through
the free, open source distribution of Cytoscape 3.3.0+ as of December 2015.
The new stringApp for Cytoscape as described and pictured in B.2. is being shared as a
free, open source app distributed through the Cytoscape App Store as of December
2015.
TRD
2.1
As mentioned in sections B.2 and B.6, our major new technologies are progressing in all
three TRDs. We are particularly excited about our precision medicine patient network
results which we hope will translate into applications in a wider set of diseases in 2016.
TRD
2.2
We anticipate that several useful resources will be generated by the proposed research.
First, the new NBS pipeline for non-coding mutations will be released and explained in
detail in our manuscript. The mutation islands, as well as their annotation, the eQTL and
HiC based networks, and the patient subtypes uncovered by NBS, will also be available.
The code used in this study will be deposited on GitHub along with tutorial
documentation.
TRD
3.2
Active Interaction Mapping technique. This technique allows the value of new interaction
mapping efforts to be rigorously evaluated rather than assumed, and the design of these
experiments can be guided rationally, based on current knowledge and data. This
technique will be publicly described in a manuscript which is currently under review.
TRD
3.3
As mentioned in sections B.2 and B.6, our major new technologies are progressing in all
three TRDs. We are particularly excited about our precision medicine patient network
results which we hope will translate into applications in a wider set of diseases in 2016.

10.
CSP
technologies
per
site:
Sander
Group
Several of the ongoing projects will make available analysis code and pipelines once
completed; in some cases, this will be done as re-usable R packages. One focus in
making projects publicly available is the development of web applications to help in the
exploration of project data. Below are some technologies that are facilitating the
development of these web applications:
• SBGNViz.js: An reusable Javascript component that allows the visualization of
detailed pathway information using SBGN in the SBGNML format,
https://github.com/nrnb/sbgnviz-js
• Shiny R Applications: One avenue for making a project publicly available is
through the use of the Shiny R web framework (produced by the RStudio
company) to quickly build web-based interfaces. This has been used by some
Sander lab projects including the CCRCC Metabolomics Data Explorer
(http://sanderlab.org/kidneyMetabProject/ related to a metabolomics project using
kidney cancer cancer samples) that includes a novel metabologram view to
highlight gene expression and metabolite changes across pathways.
The development of web applications for projects is enhanced by embeddable,
interactive components written in Javascript, such as SBGNViz.js; the possibility of
reusing these components in Shiny web applications is also possible. This is
demonstrated by the the r-cytoscape.js R package (https://github.com/cytoscape/r-
cytoscape.js) that allows users to make use of cytoscape.js in Shiny web applications to
display network data.
Bader
Group
Here below are listed two examples of additional features and application developments
that the Bader group is planning to integrate in the gene-set analysis workflow:
1) AutoAnnotate application: EnrichmentMap creates a network of enriched gene-sets
connected by overlapping genes. Similar pathways are organized in modules that
represent a common biological function. AutoAnnotate uses ClusterMaker2 to
automatically identify modules in a network, and uses WordCloud to create a label for
each module by using the most frequent words associated with the node labels of each
module. These automatic and unbiased labels help to quickly identify and visualize
biological processes represented on the network map.
2) Implementation of 2 sided Mann-Whitney test for EnrichmentMap post-analysis: post-
analysis is a feature of EnrichmentMap that enables the addition of a gene-set to an
existing EnrichmentMap network. A typical use of a 2 sided Mann-Whitney test in post-
analysis is to add a list or transcription factor of micro-RNA predicted targets as an
additional gene-set and assess the level of overlap with genes in pathways : overlap with
pathways enriched in up-regulated genes (1 side of the test) or enriched in down-
regulated genes (the other side of the test).

11.
Pico
Group
Code produced during collaborations from this period:
• New features to CentiScaPe app for Cytoscape, by Sakshi Pratap. CentiScaPe is
a popular app for Cytoscape 3 for extensive graph analysis. This was a very
successful project, with many new features added. Both mentor and student are
excited to continue Cytoscape development year-round and plan to participate in
participate in future GSoC summer programs.
https://github.com/nrnb/nrnbacademy2015sakshi
• Porting support for SBML model import and work in Cytoscape, by Matthias
König. This app, which provides SBML import and functionality to Cytoscape was
successfully completed and submitted to app store at the end of this summer,
and already has 493 downloads! A publication is in the works for this project as
well. https://github.com/nrnb/cy3sbml
• SBGNViz.js: Cytoscape.js visualization of SBGN-ML diagrams, by Metin Can
Siper. This project builds upon the cytoscape.js library to provide support for
SBGN process description notation. Some of the constributions made to this
project includes bug fixes, adding gui options, integrating a new cose layout, and
releasing version 2.4.2. https://github.com/nrnb/sbgnviz-js
• Adding PCA to clusterMaker2, by Vijay Dhameliya. This project adds principle
component analysis to the successful clusterMaker2 app, which provides over a
dozen cluster algorithms and interactive heatmap visualization.
https://github.com/nrnb/clusterMaker2
Infrastructure
technologies:
Detailed in section C.3 of the Infrastructure report are the following technologies:
• CX network interchange format
• cyWidget system
• Elsa request router
C.5.a:
Other
products
TRD
3.2
A significantly faster version of the popular random forests regression algorithm in the
Python scikit-learn package was created for this work and is publicly available on GitHub
at https://github.com/michaelkyu/scikit-learn-fasterRF.

12. E.2:
Impact
on
technology
commercialization
or
public
use
TRD
1.3
The stringApp for Cytoscape impacts the accessibility of the STRING database for
Cytoscape users. As as described and pictured in B.2, the app lets Cytoscape users
directly query and import interactions, data and annotations from the STRING database.
Infrastructure
The cytoscape.org web site is served on a virtual machine that resides on the NRNB
VMware server cluster. Cytoscape installers are staged on the standalone
chianti.ucsd.edu server, which is also sponsored by the NRNB.
The Cytoscape App Store is served on a virtual machine in the Jacobs School of
Engineering server room at UC San Diego. The NRNB pays $50 per month for this
virtual machine, and it will be transferred to NRNB servers once larger VMware servers
are purchased.
The NRNB Cluster has created a unique facility for the processing of genomic and
network computations that require dbGaP-protected data as an integral part of the
research of least 6 faculty, postdocs and graduate students. Additionally, general non-
dbGaP computations directly enable the research of another 15 postdocs and graduate
students that (because of their high processor and memory use) could not have been
performed elsewhere as cost effectively. Overall, in the last year, 90% of the cluster
nodes have been saturated with NRNB-sponsored jobs 90% of the time. Storage arrays
have ranged between 80% and 90% full.
The NRNB VMware server farm currently runs 15 virtual machines that implement
security, database and file system services, and Cytoscape CI services for the NRNB.
Executing these functions on either discrete servers or on public clouds could not have
been performed more cost effectively.