Wednesday, April 28, 2010

Open source health gadgets

Sports Watch
How would you like to have a 3-axis accelerometer, pressure sensor, temperature sensor, RF wireless, and an LCD screen in a development package? You can actually have it - as a wristwatch offered by Texas Instruments. for just $49.
The package includes a USB programming and emulation dongle so that you can develop your own firmware. It uses Texas Instrument’s SimpliciTI and BM Innovations’ Blue Robin RF protocols that enable developers to establish wireless links right out of the box. The firmware transforms it into a sports watch with heart rate monitor, it is written for Windows but could be adopted for other platforms too.
First hackers that got hold of the package used it to wirelessly unlock doors with the buttons and accelerometer. You could utilize other functionalities as well, and jog around while configuring your Linux.

Peripheral nerve stimulator

The jfish peripheral nerve stimulator is a device used in anesthesia or intensive care to assess the degree of neuromuscular blockade (normal communication between motor nerves and skeletal muscle can be blocked by a drug). The device can detect both the magnitude and type of neuromuscular blockade. Itis developed by Daniel Jolley, a doctor and anaesthetic registrar, at The Austin Hospital in Melbourne, Australia. His device uses Texas Instruments' MSP430 line of microcontrollers - ultra-low power 16-bit RISC mixed-signal computers-on-a-chip. Check the document ‘The science and use of the peripheral nerve stimulator‘ for how to use the stimulator.

Open source hardware and software solution for electrocardiography was presented at the
34th Annual Conference of the International Society for Computerized Electrocardiology
The device is battery powered, it can also use an isolation transformer plus defib protection in front of the op-amps on the front-end.

OpenEEGMany EEG-based gadgets - like Zeo personal sleep coach - are in the market. OpenEEGproject can assist your brain-computer interface, bi-directional serial communication or neurofeedback experiments. The modularEEG is currently the most popular of all the designs Check online documentation for more. Then, go to the SourceForge page and download the ModularEEG project zip-file. You will find schematics, board layouts and parts lists that can be ordered from various distributors.

What a paradise for Hackers - they can design gadgets and let other people manufacture them. The open source hardware companies are predicted to be making over one billion in revenues by 2015. Most of them are offering educational electronics, but some of the packages could be utilized for health gadget development. See this talk presented at O'Reilly's foo camp east 2010.

Open source hardware $1m and beyond - foo camp east 2010 from adafruit industries on VimReblog this post [with Zemanta]eo.

Aurametrix is working on low-cost personal diagnostic devices to improve individual health

Wednesday, April 14, 2010

AWS for Startups: what's up there in the Cloud

gSounds great, isn't it - computing services that don't need any infrastructure on your end, almost instantaneous delivery of whatever server and storage capacity you need, suite of just-right software, middleware, virtualization, security, and management tools? The "cloud" label is placed on almost every Internet-based application, adding to the large crowd of cloud computing vendors.

In a previous article, we talked about new and established players offering cloud services. This one is about cloud computing pioneer Amazon and AWS Start-Up Event in Silicon Valley (hashtag: #awsstartup_sv). See also presentation slides from their 2009, 2008 and 2007 start-up events on

The April 14th event was held at Plug and Play Tech Center

Dr. Werner Vogels, Amazon CTO, gave an overview of cloud computing. Here are a few notes taken from his talk:

Design for Automation is important, but things that are out of your control should not be automated. Examples are Human interfaces and Delete operations.
Every task should be decomposed into simpler form.
Ordering pipeline, for example, consists of cart - order - process - store - archive components that need storage and other functionality. If you decompose the pipeline into individual pieces, you will find that most of that storage is needed for particular tasks.
Good things about key value stores is that we know how to scale them. We can't do it with relational databases.
Database administration could be monotonous, overstressed, expensive. Should be more automated and scalable. Need DBA as a service.
Developer should decide how to implement services to obey regulations, failure jurisdictions, break transparency, avoid performance failures
Need evolution not revolutions.
A Virtual Private Cloud with secure VPN connection; a number of devices to have traffic routed through - such as spam, etc
Design with Security in Mind. For example, anonymous access time limit; other limits defined in scripts
Let your customer benefit.
During the past 2 years Amazon reduced pricing 6 times. Amount of bandwidth increased by orders of magnitude more than Amazon itself consumes (see this older slide showing the history of usage growth).
Amazon customers built great applications on top of AWS.
E.g., Cloudmmo - instance cloud, or cloud middleware to reduce infrastructure costs, technology risk and development time
Innovate for your customers
For example, innovate on cloud pricing models: on-demand instances; reserved instances, spot instances
Stax - elastic cloud app for J2EE
Heroku - ruby platform. maps ruby apps to amazon instances; SQL DB toolkit to build new cloud-based applications
Tibco's software helps to innovate by connecting applications and data in a service-oriented architecture, providing intelligence tools to make smarter decisions. They have templates that can be launched to cloud.
RightScale® providesfully automated management platform for Amazon EC2 cloud deployments.
Synteractive consulting and automation solutions provider, incl. CloudAdvantage

Also Netflix, Pfizer, eHarmony, Lilly, Malbec..

Pfizer uses Ec2, eHarmony uses MapReduce to find better matches.
Playfish - a fast growing social games company

Intuit - massive spiked testing with SOASTA's cloud test
Everyone files taxes at the last possible moment, so Intuit needed AWS to scale
Lots of companies use clouds for testing and simulations. Intuit simulates submitting tax forms -- if too many at a time
Ribbit; SimpleGeo; Siemens; twilio
Dr. Vogels' contact is werner at amazon or check him on twitter: @Werner

AWS Customer Presentations included VC-backed startups
@tubemogul, @rberger, @satyar73, @zynga
Adam Rose (adam at founded online video analytics startup Illumenix wich later merged with TubeMogul. The company helps in video delivery using IP and the Internet - deploying uploads and providing analytics, real-time viewership and engagement tracking.
See also useful tips from Nicolas of TubeMogul.
Robert Berger of Runa presented his company's experience with Elastic Compute Cloud, opschef and HBase, along with a few other useful AWS tips. His slides had a bit too large font size, at least for those in the front row. Guy Kawasaki says that optimal font size should be about half of the age of the oldest person in the audience. Centenarians would be certainly happy with this presentation.
A few notes I took were about Javascript for every page, every consumer, one or more AJAX calls; step function, Physical Layer; load every time a new merchant is added..
The company uses Opscode Chef for their tasks, helping to treat "Hardware"as Software .. which took under 5000 lines of ruby code
We are Living in "interesting" times with Amazon. The biggest problem is managing complexity of all the moving parts.
It's impossible to manage horizontal stacks - that's why to use Opscode Chef
there are lots of Learning Curves to Climb
Useful monitoring is hard but not critical
Satya Ramachandran of Jovian Data talked about the reasons to move to the cloud. He discussed HBase on AWS and how it may be dangerous, especially becouse of Hadoop namenode SPOF. if it went down, expect big problems
EC2 can surprise you if deploy multiple versions of horizontally scalable code
JovianData is a paltform as a service to optimize analytics of large data.
NoSQL does not solve application provision challenges
billions of impressions
10 users run 400 reports; 40% of them in hundred milliseconds
JovianData helps to avoid expensive data processing; Reduce Disk IO - by using their propriatory partitioning scheme - by materializing expensive groups (usage-based automatic view materialization).
3 main concerns:
Capital expenditure - long approval times
Over Provisioning - cluster up but nobody is using it
Application Isolation - one person runs unique report, another side section, how to isolate them to not let them run into one another
Biggest mistake - take entire image; 15 terabyte system monthly cost $30K
Role Based Clusters - example - double click services; data cleansing and creating models/ All model creation at night, than hybernated -- Hybernate Model
just kill 20 to 30 nodes; duplicate selectively then kill the nodes
ex: campaign manager needs to run lots of reports/ Classic Tera Scel won't be able to provision in minutes
Satya's advice was - If you are not getting 10x performance improvement - do not move in the clouds.
Aurametrix' comments - and if you do not need 10 or 100x improvement in performance, don't go in the cloud either. AWS is still a bit pricey for webapps and early-stage startups. Neither of the presenting startups fit the bill. A traditional VPS is a better solution if you only have hundreds or thousands of users or beta-testers. GAE is great for experimenting. Back to Satya's talk:
Dynamic Provisioning; using EC2 should be able to reduce performance by 100

Jayme Cox, talked on why Zynga chose AWS.
Zynga is conencting the world through Games. It's hosting 5 of the top 10 Facebook games
they use S3 - simple storage
Jayme Highly recommends RightScale
Scaling services without scaling Sys Admin Team
plan for success - could have 100K users
Horizontal scaling important

The 4 presenting startups also participated in

Thursday, April 8, 2010

M-health, or who will take care of me?

What is the real way to reform Health? asks Eric Wahlgren from DailyFinance, and answers 'Wireless Technology'. The coming convergence of wireless communications, social networking and medicine will transform health care agrees The Economist.

Wireless health (also called mobile health, e-health, m-health or telemedicine) will enable your body parts to make phone calls, your shoes or carpet to consult your doctor , your bed to measure your blood sugar and your phone itself to decide on whether your mental health is deteriorating - based on how quickly you answer the phone and recognize the caller.

No more lies on how much you ate or when you took your last pill. If your heart and other organs are not yet monitored by smart devices, your doctor will listen to your lungs over the phone or check how your knees are doing in 3D.

We are shifting to digital medical era starting from the relatively modest devices to keep you healthy and fit, evolving teletracking, technology, M-health sensors, Telemedicine tools and gadgets, Health 2.0 software tools, and algorithms for health data mining.

There is far more than a list of 101 things to do with a mobile phone in healthcare first compiled a year ago - including simple SMS messaging and GPS-based applications such as Medication Reminders (SMS) and Allergy Alert Service For Asthmatics (SMS and GPS), management of Chronic conditions such as Diabetes, hospital based RFID and the use of technologies such as Bluetooth and ZigBee in health and fitness monitoring.

It's time to take health care off the mainframe says Intel's Eric Dishman in his talk on
behavioral markers, vital sign monitoring and aging care delivery:

Thursday, April 1, 2010

The World of Nutritional Omics

Proteomics and Metabolomics are still lagging behind Genomics, promising to catch up in 5 or 10 years.

Nutriproteomics and Nutrimetabolomics (aka Nutritional Proteomics and Nutritional Metabolomics) may be following the same trend. According to Medline these terms are temporarily forgotten and not yet ready for the prime time.

Nutrigenomics (Nutritional Genomics) is the discipline studying the effects of food on gene expression, thought to bring technologies on tailoring diets to genetic makeups. Many researchers believe that it will also lead to creating foods (so called 'functional foods') that will prevent an individual's genes from expressing disease.

The 2006 report by GeneWatch called nutrigenomics a spin-off from the Human Genome Project created to sell the idea of 'wellness', not for improving health. This report claims that 'Personalized nutrition' is a false solution to the problem of diet-related disease. Most genetic association studies later turn out to be wrong. Genes could contribute to a person's health risks, but the number of other different factors might be overwhelming. According to this report, future health is likely to be much harder to predict than the weather is and basing diets on misleading health predictions could do more harm than good.

With the exception of the major food intolerances (for example, to milk, peanuts, fava beans and alcohol) the body's ability to respond to different diets is complex and likely to be extremely hard to predict from a person's genetic make-up. Aurametrix agrees on this with GeneWatch, but why are the weathermen still employed?.. Aurametrix bases its predictions on the body response to food intake - not only the kind that can be measured by omics technologies, but is acknowledging the importance of genome, proteome and metabolome-based diagnostics.

Like blood pressure and cholesterol levels, but unlike genetic make-up, measurements of gene expression or a person's proteome and metabolome change with time. Researchers are busily tackling transcriptome responses to foods - Dutch ServiceXS, for example, uses microarrays designed by the European Nutrigenomics Organization (NuGo) and manufactured by Affymetrix to study nutrition and genomics.
Nutrition research, on the other hand, is mostly about the isolation and analysis of bioactive components (or nutraceuticals) in foods. At first, it was focused on low molecular weight compounds and single proteins. The rapid growth of molecular biology shifted the focus to DNA, but the great expectations of solving all health-related issues by cracking the genome remained unanswered.

Genes expression does depend on diets, but mRNAs need to be translated into proteins - their sole presence does not guarantee that proteins will be present and working. Genomics fan club defines nutrigenomics as inclusive of all omics disciplines - gene, protein and metabolic profiling, but these are disciplines of their own.
Nutriproteomics studies how diets change expression, modification, distribution and interactions of proteins in the human body. It identifies the protein targets of foods and allows to more accurately than genomics address individual differences in terms of response to diet and food preference. It also helps to assess quality and authenticity of food and is useful for food allergy prevention.
Nutriproteomics addresses not only the qualitative analysis of proteomics interesting to the nutrition scientist, but also protein structures and interactions with other molecules, proteomes specific to body fluids and their localization in tissues.

In our previous blogs, we talked about metabolomics, genomics and molecular dietetics. Nutrimetabolomics focuses on the metabolomic aspect of nutritional phenotype, exploring the human response to different nutritional situations. It is estimated that there are 6,500 individual metabolites produced in the human body. Subtle disruptions in metabolic processes are evident in easily accessed body fluids and vapors. Nutrimetabolomics is nothing short of biochemical oracle for nutrition promising to accelerate the discovery of new markers and diet-related pathways. Quantitative measures of small molecules or metabolites can tell about deficiencies of digestive enzymes, microbiome health, best nutrition methods to improve individual health. Individual metabolic phenotypes do exist and can be defined from multiple measurements after eliminating the daily "noise".

The “Nutritional Phenotype database” (dbNP) was proposed to integrate and interrogate genetics, transcriptomics, proteomics, biomarkers, metabolomics, functional assays, food intake and food composition data, tailored to nutrition research and embedded in an environment of standard procedures and protocols, curated by the Nutrigenomics Organisation (NuGo). dbNP is extensively described in a publication in Genes & Nutrition 2010. It's based on micronutrient data sheets, comprehensive pathways (see examples for folate and selenium in the micronutrient portal ), ontologies and other knowledge engineering and analytic technologies.

Other Links
Aurametrix goal is to provide powerful solutions at your fingertips to help you manage your health. The company is initially focusing on relief for those suffering from digestive problems.
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