Sage Bionetworks is a non-profit organization that aims to make biomedical research more open and collaborative. It develops the Synapse platform to enable sharing of data, code, results and communication among researchers. Sage supports various research communities and projects through Synapse, including the CRC Subtyping Consortium, TCGA Pan-Cancer Consortium and Accelerating Medicines Partnership. These projects involve collaborative analysis of complex datasets toward goals like cancer subtyping and target identification for diseases.
2016 Data Commons and Data Science Workshop June 7th and June 8th 2016. Genomic Data Commons, FAIR, NCI and making data more findable, publicly accessible, interoperable (machine readable), reusable and support recognition and attribution
2016 Data Commons and Data Science Workshop June 7th and June 8th 2016. Genomic Data Commons, FAIR, NCI and making data more findable, publicly accessible, interoperable (machine readable), reusable and support recognition and attribution
dkNET Webinar: "The Microphysiology Systems Database (MPS-Db): A Platform For...dkNET
Abstract
The Microphysiology Systems Database Center (MPS-DbC) developed and implemented the Microphysiology Systems Database (MPS-Db, https://mps.csb.pitt.edu/) for the management, analysis, sharing, integration of preclinical and clinical information, and computational modeling of data in one platform, enhancing the in vitro model value and user workflow. The MPS-Db supports data from a wide range of in vitro models including static and microfluidic 2D and 3D microplates, and microfluidic MPS for single and multiple organ models. Aggregation of metadata, experimental data, and references provides for robust and relevant interpretation of the results, and having a central repository facilitates data sharing among user-specified collaborators and groups. Ready access to experimental data and metadata from any in vitro platform, along with reference data in a mineable format, provides a convenient platform for statistical analysis of performance, and building computational models to predict PK, identify compound mechanisms of actions, and infer pathways of disease progression. The MPS-DbC assists users in capturing and managing MPS data, and the MPS-Db is the central repository for the Tissue Chip Testing Centers, as well as the NCATS Tissue Chips programs. We continue to build the research and commercial value of the MPS-Db by: 1) supporting MPS users to build content; 2) implementing on-line preclinical/clinical concordance analysis capabilities; 3) enhancing the suite of data mining and computational modeling tools; and 4) augmenting methods for ensuring data quality and the secure, controlled release of data to user-specified groups.
The top 3 key questions that Microphysiology Systems Database (MPS-Db) can answer:
1. What models are available, what are their characteristics, how reproducible are they, and how can they be used?
2. How does an organ model A compare with organ model B? For example, where model A and model B are constructed in different laboratories, on different days, or with difference cells, such as iPSCs vs. primary cells.
3. Which readouts from an organ model are predictive of a specific clinical outcome and how reliable is the prediction?
Presenter: Bert Gough, PhD, Association Professor of Computational and Systems Biology, Group Leader Informatics, University of Pittsburgh Drug Discovery Institute
Upcoming webinars schedule: https://dknet.org/about/webinar
Biosecurity is often conceptualised and managed as an issue of biological risk. However, turning the focus to how to build collaboration between stakeholders in biosecurity can shed new light on why and how biosecurity surveillance programs can be successful – or not.
BioSharing - RDA Plenary 6 - Metadata Standards Catalog WG and BioSharing WG ...Peter McQuilton
An introduction to the metadata landscape in the life sciences. Covering metadata standards, the databases that implement them and the policies that endorse/recommend both standards and databases in the life sciences.
In a speech for the Global Health Program at the Council on Foreign Relations in New York City, Calit2 director Larry Smarr addresses the issue of biological diversity and the importance of monitoring the microbiome.
This presentation was provided by Leslie McIntosh of Ripeta, during the NISO hot topic event "Preprints." The virtual conference was held on April 21, 2021.
Social Machines - 2017 Update (University of Iowa)James Hendler
This is an update to the talk entitled "Social Machines: the coming collision of artificial intelligence, social networks and humanity." It was presented as an ACM Distinguished Speaker lecture at the "University of Iowa Computing Conference" 2017-02-24
AWS re:Invent 2016: Building a Platform for Collaborative Scientific Research...Amazon Web Services
This session discusses the architecture, formation, and usage of a collaborative HPC/big data scientific research and analysis environment on AWS. The pharmaceutical industry trend toward joint ventures and collaborations has created a need for new platforms in which to work together. We'll dive into architectural decisions for building collaborative systems. Examples include how such a platform allowed Human Longevity, Inc. to accelerate software deployment to production in a fast-paced research environment, and how Celgene uses AWS for research collaboration with outside universities and foundations.
dkNET Webinar: "The Microphysiology Systems Database (MPS-Db): A Platform For...dkNET
Abstract
The Microphysiology Systems Database Center (MPS-DbC) developed and implemented the Microphysiology Systems Database (MPS-Db, https://mps.csb.pitt.edu/) for the management, analysis, sharing, integration of preclinical and clinical information, and computational modeling of data in one platform, enhancing the in vitro model value and user workflow. The MPS-Db supports data from a wide range of in vitro models including static and microfluidic 2D and 3D microplates, and microfluidic MPS for single and multiple organ models. Aggregation of metadata, experimental data, and references provides for robust and relevant interpretation of the results, and having a central repository facilitates data sharing among user-specified collaborators and groups. Ready access to experimental data and metadata from any in vitro platform, along with reference data in a mineable format, provides a convenient platform for statistical analysis of performance, and building computational models to predict PK, identify compound mechanisms of actions, and infer pathways of disease progression. The MPS-DbC assists users in capturing and managing MPS data, and the MPS-Db is the central repository for the Tissue Chip Testing Centers, as well as the NCATS Tissue Chips programs. We continue to build the research and commercial value of the MPS-Db by: 1) supporting MPS users to build content; 2) implementing on-line preclinical/clinical concordance analysis capabilities; 3) enhancing the suite of data mining and computational modeling tools; and 4) augmenting methods for ensuring data quality and the secure, controlled release of data to user-specified groups.
The top 3 key questions that Microphysiology Systems Database (MPS-Db) can answer:
1. What models are available, what are their characteristics, how reproducible are they, and how can they be used?
2. How does an organ model A compare with organ model B? For example, where model A and model B are constructed in different laboratories, on different days, or with difference cells, such as iPSCs vs. primary cells.
3. Which readouts from an organ model are predictive of a specific clinical outcome and how reliable is the prediction?
Presenter: Bert Gough, PhD, Association Professor of Computational and Systems Biology, Group Leader Informatics, University of Pittsburgh Drug Discovery Institute
Upcoming webinars schedule: https://dknet.org/about/webinar
Biosecurity is often conceptualised and managed as an issue of biological risk. However, turning the focus to how to build collaboration between stakeholders in biosecurity can shed new light on why and how biosecurity surveillance programs can be successful – or not.
BioSharing - RDA Plenary 6 - Metadata Standards Catalog WG and BioSharing WG ...Peter McQuilton
An introduction to the metadata landscape in the life sciences. Covering metadata standards, the databases that implement them and the policies that endorse/recommend both standards and databases in the life sciences.
In a speech for the Global Health Program at the Council on Foreign Relations in New York City, Calit2 director Larry Smarr addresses the issue of biological diversity and the importance of monitoring the microbiome.
This presentation was provided by Leslie McIntosh of Ripeta, during the NISO hot topic event "Preprints." The virtual conference was held on April 21, 2021.
Social Machines - 2017 Update (University of Iowa)James Hendler
This is an update to the talk entitled "Social Machines: the coming collision of artificial intelligence, social networks and humanity." It was presented as an ACM Distinguished Speaker lecture at the "University of Iowa Computing Conference" 2017-02-24
AWS re:Invent 2016: Building a Platform for Collaborative Scientific Research...Amazon Web Services
This session discusses the architecture, formation, and usage of a collaborative HPC/big data scientific research and analysis environment on AWS. The pharmaceutical industry trend toward joint ventures and collaborations has created a need for new platforms in which to work together. We'll dive into architectural decisions for building collaborative systems. Examples include how such a platform allowed Human Longevity, Inc. to accelerate software deployment to production in a fast-paced research environment, and how Celgene uses AWS for research collaboration with outside universities and foundations.
Presentation to clinicians on what they need to think about to do a large-scale Open Science project where they want to share clinical, genomic and imaging data.
Building a Network of Interoperable and Independently Produced Linked and Ope...Michel Dumontier
Over 15 years ago, Sir Tim Berners Lee proclaimed the founding of an exciting new future involving intelligent agents operating over smarter data in order to perform complex tasks at the behest of their human controllers. At the heart of this vision lies an uneasy alliance between tedious formal knowledge representations and powerful analytics over big, but often messy data. Bio2RDF, our decade old open source project to create Linked Data for the life sciences, has weaved emergent Semantic Web technologies such as ontologies and Linked Data to generate FAIR - Findable, Accessible, Interoperable, and Reusable - data in the form of billions of machine accessible statements for use in downstream biomedical discovery.
This revolution in data publication has been strengthened by action from global bioinformatics institutions such as the NCBI, NCBO, EBI, and DBCLS. Notably, NCBI's PubChem has successfully coupled large scale data integration with community-based standards to offer a remakable biochemical knowledge resource amenable to data hungry discovery tools. Yet, in the face of increasing pressure from researchers, funders, and publishers, will these approaches be sufficient for growing and maintaining a comprehensive knowledge graph that is inclusive of all biomedical research?
Thesis defense, Heather Piwowar, Sharing biomedical research dataHeather Piwowar
Presentation by Heather Piwowar as PhD dissertation defense on March 24, 2010 at the Dept of Biomedical Informatics, U of Pittsburgh. "Foundational studies for
measuring the impact, prevalence, and patterns of publicly sharing biomedical research data." I passed :)
Branch: An interactive, web-based tool for building decision tree classifiersBenjamin Good
A crucial task in modern biology is the prediction of complex phenotypes, such as breast cancer prognosis, from genome-wide measurements. Machine learning algorithms can sometimes infer predictive patterns, but there is rarely enough data to train and test them effectively and the patterns that they identify are often expressed in forms (e.g. support vector machines, neural networks, random forests composed of 10s of thousands of trees) that are highly difficult to understand. In addition, it is generally unclear how to include prior knowledge in the course of their construction.
Decision trees provide an intuitive visual form that can capture complex interactions between multiple variables. Effective methods exist for inferring decision trees automatically but it has been shown that these techniques can be improved upon via the manual interventions of experts. Here, we introduce Branch, a new Web-based tool for the interactive construction of decision trees from genomic datasets. Branch offers the ability to: (1) upload and share datasets intended for classification tasks (in progress), (2) construct decision trees by manually selecting features such as genes for a gene expression dataset, (3) collaboratively edit decision trees, (4) create feature functions that aggregate content from multiple independent features into single decision nodes (e.g. pathways) and (5) evaluate decision tree classifiers in terms of precision and recall. The tool is optimized for genomic use cases through the inclusion of gene and pathway-based search functions.
Branch enables expert biologists to easily engage directly with high-throughput datasets without the need for a team of bioinformaticians. The tree building process allows researchers to rapidly test hypotheses about interactions between biological variables and phenotypes in ways that would otherwise require extensive computational sophistication. In so doing, this tool can both inform biological research and help to produce more accurate, more meaningful classifiers.
A prototype of Branch is available at http://biobranch.org/
Scott Edmunds: GigaScience - a journal or a database? Lessons learned from th...GigaScience, BGI Hong Kong
Scott Edmunds talk at the HUPO congress in Geneva, September 6th 2011 on GigaScience - a journal or a database? Lessons learned from the Genomics Tsunami.
Access the webinar: http://goo.gl/p08pTz
These slides were presented in a webinar by Denodo in collaboration with BioStorage Technologies and Indiana Clinical and Translational Sciences Institute and Regenstrief Institute.
BioStorage Technologies, Inc., Indiana Clinical and Translational Sciences Institute, and Regenstrief Institute (CTSI) have joined Denodo to talk about the important role of technological advancements, such as data virtualization, in advancing biospecimen research.
By watching this webinar, you can gain insight into best practices around the integration of biospecimen and research data as well as technology solutions that provide consolidated views and rapid conversions of this data into valuable business insights. You will also learn how data virtualization can assist with the integration of data residing in heterogeneous repositories and can securely deliver aggregated data in real-time.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
leveraging the web to make science more collaborative
1. Synapse
leveraging the web to make science more collaborative
brian m. bot | sage bionetworks | @BrianMBot
2. sage bionetworks
35 FTEs - hiring 5 additional
1/2 research - 1/3 platform - 1/6 leadership & support
3. sage bionetworks
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
supports communities of researchers
working collaboratively across disciplines
4. sage bionetworks
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
13. sage bionetworks
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
supports communities of researchers
working collaboratively across disciplines
15. sage bionetworks
enables sharing of all resources (data, code, results)
and their relationships to one another
multi-channel communication
instead of uni-directional broadcasting
aides in reproducibility by
enabling communication throughout the research process
not only at time of publication
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
16. sage bionetworks
distributed & versioned file system
rich annotations (metadata)
customizable schemas for structured data
agnostic to storage solution (cloud, local server, etc.)
wiki authoring
access controls (share whatever with whomever)
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
17. sage bionetworks
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
open RESTful APIs
www.synapse.org
programmatic clients
18. sage bionetworks
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
User
registra*on/cer*fica*on
User
agreement
to
Terms
and
Condi*ons
of
Use
Data
Use
Procedure
Data
privacy
Policy
Removal
of
direct
iden*fiers
Tier
access
Login
requirement,
encryp*on
in
and
out,
firewalls
IT
policy
Training-‐
Audi*ng-‐
Monitoring
Consequences
for
viola*on
(inten*onal
or
not)
Synapse Governance
a complete process
19. sage bionetworks
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
supports communities of researchers
working collaboratively across disciplines
23. DREAM Challenges
Columbia Professor Dimitris Anastassiou
MPEG-2 compression of digital audio and video signals
Modules of co-expressed genes shared across cancers
Belief that these ‘attractors’ represent underlying biological
mechanisms (bioinformatic ‘hallmarks of cancer’1)
1D. Hanahan, R. A. Weinberg. Hallmarks of cancer: The next generation. Cell 144, 646–674 (2011)
28. Accelerating Medicines Partnership
biopharma
AbbVie
Biogen Idec
Bristol-Myers Squibb
GlaxoSmithKline
Johnson & Johnson
Lilly
Merck
Pfizer
Sanofi
Takeda
non-profit
Alzheimer’s Association
Alzheimer’s Drug Discovery Foundation
American Diabetes Association
Arthritis Foundation
Foundation for the NIH
Geoffrey Beene Foundation
Juvenile Diabetes Research Foundation
Lupus Foundation of America
Lupus Research Institute/Alliance for Lupus Research
PhRMA
Rheumatology Research Foundation
USAgainstAlzheimer’s
29. Accelerating Medicines Partnership
($ Millions)
Total
Project
Total NIH
Total
Industry
Alzheimer’s
Disease
129.5 67.6 61.9
Type 2
Diabetes
58.4 30.4 28
Rheumatoid
Arthritis
41.6 20.9 20.7
TOTAL 229.5 118.9 110.6
30. Accelerating Medicines Partnership
cross-project data generation
shRNA
compounds
RNAi
human
mouse
drosophila
iPSC
RNA-seq
Whole exome
WGS
methylation
miRNA
proteomics
phenotypic measurements
modificationssystems data generation
X X
46. Synapse
leveraging the web to make science more collaborative
brian m. bot
m1-a111
brian.bot@sagebase.org
@BrianMBot
Synapse engineering team
Michael Kellen, Director
Christopher Bare
Marcel Blonk
John Hill
Jay Hodgson
Bruce Hoff
Xavier Schildwachter