Tag Archives: Cloud

Digital health exchange #healthxchange innovation session

This morning I am at the digital health exchange panel session in Arlington, VA.

Panel Moderator: Mark Naggar, Project Manager, HHS Buyers Club (HHS IDEA Lab) – Office of the Chief Technology Officer, Department of Health and Human Services (confirmed)

  1. Dr. Neil Evans is a board-certified, Co-Director of Connected Health, aligned under the Office of Informatics and Analytics, in the Veterans Health Administration within the U.S. Department of Veterans Affairs and practicing primary care internist at the Washington, D.C. Veterans Affairs Medical Center. Dr. Evans co-leads the effort to improve services to Veterans, their families and Caregivers by increasing access, fostering continuity and promoting patient empowerment through electronic health technologies wth a focus on mobile and digital health.  (confirmed)
  2. Kathryn Wetherby serves as a Public Health Advisor at the Substance Abuse and Mental Health Services Administration (SAMHSA)where she leads large health information technology projects and contracts. Ms. Wetherby has over 16 years of experience in both the public and private sectors; including implementation of large scale, enterprise-wide health information technology systems, mobile technologies, standards, strategic planning and organization and operational change. (confirmed)
  3. Justin Woodson is an Associate Professor, Uniformed Services University Health Services (USUHS), the institution charged with training, educating and preparing officers and leaders to directly support the Military Health System, the National Security and National Defense Strategies of the United States and the readiness of our Armed Forces. (confirmed)
  4. Joe Klosky, Senior Technical Advisor, Food and Drug Administration.   Having previously served as the Chief Technology Officer for the FDA in 2007, Mr. Klosky has supported a number of initiatives across HHS, including a detail to the to the NIH CIO and Chief Enterprise Architect. Mr. Klosky recently rejoined the FDA as a senior technical advisor in support of HHS wide work groups and projects. (confirmed)

 

The panelist roles and perspective:

Dr.Neil Evans – connected health covers all technology outside the face to face engagement for veterans.

Connected health runs the VA innovation competitions.

Kate Wetherby – leads health it projects including mobile apps and portals and solutions for outreach in rural areas.

Justin Woodson – innovating by “getting out of the box”. Justin is based in the military medical school. Role in innovation is to create unique experiences at the intersection of military and academia. Building interactive experiences.

Joe Klosky – FDA: troubleshooter – “into the breach”. Using Amazon cloud at FDA. Handling very sensitive data.

Mark Naggar – HHS is trying to develop a more collaborative and innovative ecosystem. HHS has its own internal accelerator.

Q: what organizations do the panelists admire for innovation?

Justin W: private organizations have more flexibility to acquire talent and apply it. Organizations like Google are willing to take risks.

Neil E: Procter & Gamble mixes employees across divisions. They expected people to take time out of their normal duties to mingle with colleagues from other divisions and to share ideas.

Justin W/Neil E: medicine tends to work in silos. More effort is needed to make inter-disciplinary interactions happen. This has to tap the people in the field that are doing the work.

Joe K:  use commercial tools to help collaboration happen. Also mingle commercial tools to create new solutions.

Kate W: combatting the “we have always done it this way”. You need to have people to drive the change.

Mark N: HHS has implemented the entrepreneur-in-Residence program. Unfortunately they are restricted from bringing people from for-profit companies. But people are trying to figure out how to do this.

Q: where have you gone from concept to execution successfully – or what have you learned from a failure to get to execution.

Neil E: VA has entrepreneur in residence. Last year they were able to partner with Walgreens to help veterans get their flu vaccine and have the data fly in to the Vista EHR.  After a pilot in 2013 this was rolled out across the country this year.

Choose a project with a hard deadline. Eg. There is a deadline for flu vaccines.

Even simple projects can require innovative approaches.

The va mail pharmacy implemented a system to allow veterans to track their medications through the mail system.

Justin W: innovation does not have to be new. It can be a mashup of existing solutions to solve a problem. Taking existing ideas in to a new realm.

Kate W: Consent to Share – working on interoperability. Dealing with privacy and security regulations. Working on data segmentation privacy and consent to share. Parse the medical record and segment it to allow the patient to share sub-sections of their health record. There are issues with sharing certain health data. Variations at the state level.

SAMSHA has built this in to a PHR. Cerner and nexgen have done similar work. HHS has shown the direction and is encouraging others to build on what they have done for data segmentation.

Joe K: FDA is at every custom station. It is a massive undertaking. Working on a risk based model. Applying technology eg. Forensic technology lab in Cleveland. Technology is being used to handle globalization despite budget constraints.

Q: what barrier would you remove to improve the path to innovation?:

Justin W: change the manning model.

Joe K: the procurement process around innovation while complying with FAR

Neil E: in IT rules applied for production but need simpler!more agile approaches for pilots.

Kate W: workforce development to prep people for technology use.

Justin W:  focus on leadership development that includes innovation as a leadership responsibility.

Neil E: VA annual innovation competition. It creates community. Ideas get voted on and commented on. The comment process creates communities of interest.

Q: How do small businesses with innovative ideas partner with the agencies.

HHS has s&i framework committed and other work groups. There are a lot of open forums and information on HHS web sites.

Big challenge is to educate and communicate to the workforce about new innovations.

Kate W: project Echo – using Telehealth for workforce training.

 

Mark Scrimshire
HHS Entrepreneur-in-Residence at CMS building BlueButton Plus for Medicare.
Mark is available for challenging assignments at the intersection of Health and Technology using Big Data, Mobile and Cloud Technologies. If you need help to move, or create, your health applications in the cloud let’s talk.
Stay up-to-date: Twitter @ekivemark
Disclosure: I began as a Patient Engagement Advisor and am now CTO to Personiform, Inc. and their Medyear.com platform. Medyear is a powerful free tool that helps you collect, organize and securely share health information, however you want.  Manage your own health records today. Medyear: Less hassle. Better care.

Updated:Building a Healthcare Big Data Platform in the Cloud with @Datastax

Update: The date of the Webinar has been changed to: monday August 18th.

On August 18th, at Noon ET, I will be presenting on a Webinar with Datastax about building a Cloud-based Big Data platform for the Healthcare software division of Fortune 50 company using Datastax.

You can sign up for the webinar here: http://learn.datastax.com/WebinarDataStaxEnterpriseintheCloudHowthisFortune50HealthcareCompanyTurnedBigDataintoBigAnswers.html?utm_source=web&utm_medium=resources&utm_campaign=gtro4

This webinar will bring the presentation I delivered to a group in Boston, in May 2014, to a wider audience. I hope you can join me.

#MongoDBWorld Genomics and the Connectivity Map (A presentation from the Broad Institute)

More from #MongoDBWorld.

Presentation by the Broad Institute:

# MongoDB and the Connectivity Map: Making Connections Between Genetics and Disease

“The Broad Institute has developed a novel high-throughput gene-expression profiling technology and has used it to build an open-source catalog of over a million profiles that captures the functional states of cells when treated with drugs and other types of perturbations. Referred to as the Connectivity Map (or CMap), these data when paired with pattern matching algorithms, facilitate the discovery of connections between drugs, genes and diseases. We wished to expose this resource to scientists around the world via an API that is easily accessible to programmers and biologists alike. We required a database solution that could handle a variety of data types and handle frequent changes to the schema. We realized that a relational database did not fit our needs, and gravitated towards MongoDB for its ease of use, support for dynamic schema, complex data structures and expressive query syntax. In this talk, we’ll walk through how we built the CMap library. We’ll discuss why we chose MongoDB, the various schema design iterations and tradeoffs we’ve made, how people are using the API, and what we’re planning for the next generation of biomedical data.”

https://world.mongodb.com/mongodb-world/session/mongodb-and-connectivity-map-making-connections-between-genetics-and-disease

The Connectivity Map began as a pilot project in 2006.

7,000 experiments
19,000 registered users
1,200 Scientific Reports

One Gene expression signature is expensive – thousands of dollars.

As cost drops the number of experiments can increase.

This has grown to 1.5 million experiments.

MongoDB came in to play because they didn’t know what the data structures needed to be.

CMap LINCS Dataset has built a library of 1.4M gene expression profiles.
12,488 compounds,

The Connectivity Map is easy to describe but difficult to model.

1.4 M profiles times 22,000 geners yields 30B data points.

This is further complicated by the diversity of use cases and users.

Annotation is complex and may be partial. The data is also frequently updated.

The Agile approach:
– Store just what’s needed
– Test and use daily
– Refactor frequently

The initial data model was simply an inventory of signatures.

4-5 fields in a json data packet.
This evolved from a simple signature_info block to cell_info and Treatment_info.

They then added computed fields and external meta-data which were added to Singature_info and Cell_info. This is easy to do in MongoDB.

APIs are awesome! Life Sciences need more of them.

functionality in the API overcame convention. So used the ?siginfo?q={“cell”:”A”} style rather than folder convention /siginfo/cell/A

Node.js and Mongoose (as noted in the earlier LinkedIn session) came in to play for easy API creation.

Compute API running on AWS performs message queuing via a capped collection.

HDF5 (Hierarchical Data Format) complements MongoDB for numerical analysis

GCTX is a binary format based on HDF5, cross platform with multiple language bindings.

Broad’s platform is Lincscloud – targeted to researchers: Lincsloud.org
This is free for academic use.

Uses of Broad’s tools:

  • Predicting Drug Function
  • Drug Re-purposing (failed drugs – new uses)
    i.e. Phase 2 trials are where results don’t live up to expectations but DRUG IS SAFE!

So can drug be re-mapped to new targets.
– Pushing from single patient application to two patients and on to population applications.

[tag health cloud BigData MongoDB MongoDBWorld NoSQL]

Mark Scrimshire
Health & Cloud Technology Consultant

Mark is available for challenging assignments at the intersection of Health and Technology using Big Data, Mobile and Cloud Technologies. If you need help to move, or create, your health applications in the cloud let’s talk.
Blog: http://blog.ekivemark.com
email: mark
Stay up-to-date: Twitter @ekivemark
Disclosure: I began as a Patient Engagement Advisor and am now CTO to Personiform, Inc. and their Medyear.com platform. Medyear is a powerful free tool that helps you collect, organize and securely share health information, however you want. Manage your own health records today. Medyear: The Power Grid for your Health.

#MongoDBWorld Hidden gems in the new 2.6 version of @mongoDB

More from #MongoDBWorld.

Hidden Gems in the 2.6 Release

Everyone using MongoDB is familiar with the big features of the 2.6 release (and if you’re not, here’s a link) — text search, $out, user-defined roles, X509 authentication, etc. But what about the little guys? Our VP of Engineering, Daniel Pasette, will take you on a tour of five small but mighty features from the 2.6 release that make your MongoDB experience more productive.

Dan Pasette

VP of Core Engineering at MongoDB

Dan is the VP of Core Engineering at MongoDB. Prior to joining MongoDB, Dan was a Development Manager at LimeWire where he led a team working on content ingestion for an (unreleased) digital music service called Grapevine. Past employment includes MTV Networks, Sonicnet, iXL, and Electronic Book Technologies. Dan holds a degree in Computer Science from Brown University.

http://world.mongodb.com/mongodb-world/session/hidden-gems-26-release

The Technical sessions are packed. I was hoping to look at Memory Management but the room was full to overflowing. So I dropped in to the session on the latest release of MongoDB – Version 2.6.

Power of 2 – Now default allocation Strategy

Power of 2 feature allows extra space when saving records. It is on by default in the latest release. It is best suited to uses that have re-writes to databases. What typically happens is a re-write expands the file and the file wouldn’t fit in the existing space. The extra space enabled by Power of 2 makes it more likely that records can be written back to the blocks they came from.

By adding space to records it reduces the amount of data movement because as data grows inside records the records still fit.

Server Side Timeouts

An example, a collection was indexed in staging but forgotten in production. This can cause table scans that cause users to re-try or re-scan. This creates socket timeouts. This can impact other users on the system. The new feature is maxTimeMS. This allows you to set a maximum time for how long an operation can run in the database. Set from milliseconds to minutes depending on the operation.

Query Engine Introspection

This works in conjunction with MaxTimeMS. It allows you to delve in to queries to resolve problems. The Query execution framework was completely re-writtin in 2.6. Prior to 2.6 the query path etc was opaque to users. This changed in 2.6.

The Query Planner chooses the best index for a given query.

Query Parser sends to Query Planner. This is passed to the Plan Cache. which passes to the Plan Runner.

The Plan Enumerator passes all the plans to the Multiplan router. This runs these plans for a limited amount of time and then chooses the most efficient.

On subsequent execution of the same query the query goes straight to the Plan Cache.

If the plan caches a sub-optimal plan.
Plans are dropped after indexing and other major changes.

getPlanCache

A set of Plan Cache tools to view and manipulate the cache.

Background indexing on Secondaries

This has existed but the feature has been rounded out.

Pre-2.6 background index builds became foreground index builds when replicated to secondaries.

In 2.6 keeps background indexing in the background.
Note: Background indexing isn’t as fast and is less tightly packed.

User Driven Enhancements

All of these features came about as a result of user feedback that go through jira.mongodb.com

Limits on Replica sets

Limit of 12 nodes in a replica set with 7 voting members

[tag cloud BigData MongoDBWorld

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Mark Scrimshire
Health & Cloud Technology Consultant

Mark is available for challenging assignments at the intersection of Health and Technology using Big Data, Mobile and Cloud Technologies. If you need help to move, or create, your health applications in the cloud let’s talk.
Blog: http://blog.ekivemark.com
email: mark@ekivemark.com
Stay up-to-date: Twitter @ekivemark
Disclosure: I began as a Patient Engagement Advisor and am now CTO to Personiform, Inc. and their Medyear.com platform. Medyear is a powerful free tool that helps you collect, organize and securely share health information, however you want. Manage your own health records today. Medyear: The Power Grid for your Health.