Forget Apple Watch and Fitbit — if we’re going to wear something electronic, we want to make it ourselves!
Wearable Tech Projects, from the makers of HackSpace magazine, is a 164-page book packed with projects for the fashionable electronics enthusiast, with more than 30 projects which will blink, flash, and spark joy in your life.
Make a wearable game controller
Fans of Sophy Wong will already know about the amazing wearable tech that she develops. We wanted to make sure that more people discovered her work and the incredible world of wearable technology. You’ll start simple with sewable circuits and LEDs, and work all the way up to building your own wearable controller (complete with feathers) for an interactive, fully immersive game of Flappy Bird.
Pick up the tricks of the trade
Along the way, you’ll embed NFC data in a pair of cufflinks, laser cut jewellery, 3D print LED diffusers onto fabric for a cyberpunk leather jacket, and lots more.
Learn new techniques from Sophy Wong
You’ll discover new techniques for working with fabric, find out about the best microcontrollers for your projects, and learn the basics of CircuitPython, the language developed at Adafruit for physical computing. There’s no ‘Hello, World!’ or computer theory here; this is all about practical results and making unique, fascinating things to wear.
Get your copy today
Wearable Tech Projects is available to buy online for £10 with free delivery. You can also get it from WHSmith and all the usual high street retail suspects.
This blog post was co-authored by Ujjwal Ratan, a senior AI/ML solutions architect on the global life sciences team.
Healthcare data is generated at an ever-increasing rate and is predicted to reach 35 zettabytes by 2020. Being able to cost-effectively and securely manage this data whether for patient care, research or legal reasons is increasingly important for healthcare providers.
Healthcare providers must have the ability to ingest, store and protect large volumes of data including clinical, genomic, device, financial, supply chain, and claims. AWS is well-suited to this data deluge with a wide variety of ingestion, storage and security services (e.g. AWS Direct Connect, Amazon Kinesis Streams, Amazon S3, Amazon Macie) for customers to handle their healthcare data. In a recent Healthcare IT News article, healthcare thought-leader, John Halamka, noted, “I predict that five years from now none of us will have datacenters. We’re going to go out to the cloud to find EHRs, clinical decision support, analytics.”
I realize simply storing this data is challenging enough. Magnifying the problem is the fact that healthcare data is increasingly attractive to cyber attackers, making security a top priority. According to Mariya Yao in her Forbes column, it is estimated that individual medical records can be worth hundreds or even thousands of dollars on the black market.
In this first of a 2-part post, I will address the value that AWS can bring to customers for ingesting, storing and protecting provider’s healthcare data. I will describe key components of any cloud-based healthcare workload and the services AWS provides to meet these requirements. In part 2 of this post we will dive deep into the AWS services used for advanced analytics, artificial intelligence and machine learning.
The data tsunami is upon us
So where is this data coming from? In addition to the ubiquitous electronic health record (EHR), the sources of this data include:
devices such as MRIs, x-rays and ultrasounds
sensors and wearables for patients
medical equipment telemetry
Additional sources of data come from non-clinical, operational systems such as:
claims and billing
Data from these sources can be structured (e.g., claims data) as well as unstructured (e.g., clinician notes). Some data comes across in streams such as that taken from patient monitors, while some comes in batch form. Still other data comes in near-real time such as HL7 messages. All of this data has retention policies dictating how long it must be stored. Much of this data is stored in perpetuity as many systems in use today have no purge mechanism. AWS has services to manage all these data types as well as their retention, security and access policies.
Imaging is a significant contributor to this data tsunami. Increasing demand for early-stage diagnoses along with aging populations drive increasing demand for images from CT, PET, MRI, ultrasound, digital pathology, X-ray and fluoroscopy. For example, a thin-slice CT image can be hundreds of megabytes. Increasing demand and strict retention policies make storage costly.
Due to the plummeting cost of gene sequencing, molecular diagnostics (including liquid biopsy) is a large contributor to this data deluge. Many predict that as the value of molecular testing becomes more identifiable, the reimbursement models will change and it will increasingly become the standard of care. According to the Washington Post article “Sequencing the Genome Creates so Much Data We Don’t Know What to do with It,”
“Some researchers predict that up to one billion people will have their genome sequenced by 2025 generating up to 40 exabytes of data per year.”
Although genomics is primarily used for oncology diagnostics today, it’s also used for other purposes, pharmacogenomics — used to understand how an individual will metabolize a medication.
It is increasingly challenging for the typical hospital, clinic or physician practice to securely store, process and manage this data without cloud adoption.
Amazon has a variety of ingestion techniques depending on the nature of the data including size, frequency and structure. AWS Snowball and AWS Snowmachine are appropriate for extremely-large, secure data transfers whether one time or episodic. AWS Glue is a fully-managed ETL service for securely moving data from on-premise to AWS and Amazon Kinesis can be used for ingesting streaming data.
Amazon S3, Amazon S3 IA, and Amazon Glacier are economical, data-storage services with a pay-as-you-go pricing model that expand (or shrink) with the customer’s requirements.
The above architecture has four distinct components – ingestion, storage, security, and analytics. In this post I will dive deeper into the first three components, namely ingestion, storage and security. In part 2, I will look at how to use AWS’ analytics services to draw value on, and optimize, your healthcare data.
A typical provider data center will consist of many systems with varied datasets. AWS provides multiple tools and services to effectively and securely connect to these data sources and ingest data in various formats. The customers can choose from a range of services and use them in accordance with the use case.
For use cases involving one-time (or periodic), very large data migrations into AWS, customers can take advantage of AWS Snowball devices. These devices come in two sizes, 50 TB and 80 TB and can be combined together to create a petabyte scale data transfer solution.
The devices are easy to connect and load and they are shipped to AWS avoiding the network bottlenecks associated with such large-scale data migrations. The devices are extremely secure supporting 256-bit encryption and come in a tamper-resistant enclosure. AWS Snowball imports data in Amazon S3 which can then interface with other AWS compute services to process that data in a scalable manner.
For use cases involving a need to store a portion of datasets on premises for active use and offload the rest on AWS, the Amazon storage gateway service can be used. The service allows you to seamlessly integrate on premises applications via standard storage protocols like iSCSI or NFS mounted on a gateway appliance. It supports a file interface, a volume interface and a tape interface which can be utilized for a range of use cases like disaster recovery, backup and archiving, cloud bursting, storage tiering and migration.
By using the AWS proposed reference architecture for disaster recovery, healthcare providers can ensure their data assets are securely stored on the cloud and are easily accessible in the event of a disaster. The “AWS Disaster Recovery” whitepaper includes details on options available to customers based on their desired recovery time objective (RTO) and recovery point objective (RPO).
AWS is an ideal destination for offloading large volumes of less-frequently-accessed data. These datasets are rarely used in active compute operations but are exceedingly important to retain for reasons like compliance. By storing these datasets on AWS, customers can take advantage of the highly-durable platform to securely store their data and also retrieve them easily when they need to. For more details on how AWS enables customers to run back and archival use cases on AWS, please refer to the following set of whitepapers.
A healthcare provider may have a variety of databases spread throughout the hospital system supporting critical applications such as EHR, PACS, finance and many more. These datasets often need to be aggregated to derive information and calculate metrics to optimize business processes. AWS Glue is a fully-managed Extract, Transform and Load (ETL) service that can read data from a JDBC-enabled, on-premise database and transfer the datasets into AWS services like Amazon S3, Amazon Redshift and Amazon RDS. This allows customers to create transformation workflows that integrate smaller datasets from multiple sources and aggregates them on AWS.
Healthcare providers deal with a variety of streaming datasets which often have to be analyzed in near real time. These datasets come from a variety of sources such as sensors, messaging buses and social media, and often do not adhere to an industry standard. The Amazon Kinesis suite of services, that includes Amazon Kinesis Streams, Amazon Kinesis Firehose, and Amazon Kinesis Analytics, are the ideal set of services to accomplish the task of deriving value from streaming data.
Example: Using AWS Glue to de-identify and ingest healthcare data into S3 Let’s consider a scenario in which a provider maintains patient records in a database they want to ingest into S3. The provider also wants to de-identify the data by stripping personally- identifiable attributes and store the non-identifiable information in an S3 bucket. This bucket is different from the one that contains identifiable information. Doing this allows the healthcare provider to separate sensitive information with more restrictions set up via S3 bucket policies.
To ingest records into S3, we create a Glue job that reads from the source database using a Glue connection. The connection is also used by a Glue crawler to populate the Glue data catalog with the schema of the source database. We will use the Glue development endpoint and a zeppelin notebook server on EC2 to develop and execute the job.
Step 1: Import the necessary libraries and also set a glue context which is a wrapper on the spark context:
Step 2: Create a dataframe from the source data. I call the dataframe “readmissionsdata”. Here is what the schema would look like:
Step 3: Now select the columns that contains indentifiable information and store it in a new dataframe. Call the new dataframe “phi”.
Step 4: Non-PHI columns are stored in a separate dataframe. Call this dataframe “nonphi”.
Step 5: Write the two dataframes into two separate S3 buckets
Once successfully executed, the PHI and non-PHI attributes are stored in two separate files in two separate buckets that can be individually maintained.
In 2016, 327 healthcare providers reported a protected health information (PHI) breach, affecting 16.4m patient records. There have been 342 data breaches reported in 2017 — involving 3.2 million patient records.
To date, AWS has released 51 HIPAA-eligible services to help customers address security challenges and is in the process of making many more services HIPAA-eligible. These HIPAA-eligible services (along with all other AWS services) help customers build solutions that comply with HIPAA security and auditing requirements. A catalogue of HIPAA-enabled services can be found at AWS HIPAA-eligible services. It is important to note that AWS manages physical and logical access controls for the AWS boundary. However, the overall security of your workloads is a shared responsibility, where you are responsible for controlling user access to content on your AWS accounts.
AWS storage services allow you to store data efficiently while maintaining high durability and scalability. By using Amazon S3 as the central storage layer, you can take advantage of the Amazon S3 storage management features to get operational metrics on your data sets and transition them between various storage classes to save costs. By tagging objects on Amazon S3, you can build a governance layer on Amazon S3 to grant role based access to objects using Amazon IAM and Amazon S3 bucket policies.
To learn more about the Amazon S3 storage management features, see the following link.
In the example above, we are storing the PHI information in a bucket named “phi.” Now, we want to protect this information to make sure its encrypted, does not have unauthorized access, and all access requests to the data are logged.
Encryption: S3 provides settings to enable default encryption on a bucket. This ensures any object in the bucket is encrypted by default.
Logging: S3 provides object level logging that can be used to capture all API calls to the object. The API calls are logged in cloudtrail for easy access and consolidation. Moreover, it also supports events to proactively alert customers of read and write operations.
Access control: Customers can use S3 bucket policies and IAM policies to restrict access to the phi bucket. It can also put a restriction to enforce multi-factor authentication on the bucket. For example, the following policy enforces multi-factor authentication on the phi bucket:
In Part 1 of this blog, we detailed the ingestion, storage, security and management of healthcare data on AWS. Stay tuned for part two where we are going to dive deep into optimizing the data for analytics and machine learning.
A couple of weekends ago, we celebrated our sixth birthday by coordinating more than 100 simultaneous Raspberry Jam events around the world. The Big Birthday Weekend was a huge success: our fantastic community organised Jams in 40 countries, covering six continents!
We sent the Jams special birthday kits to help them celebrate in style, and a video message featuring a thank you from Philip and Eben:
To celebrate the Raspberry Pi’s sixth birthday, we coordinated Raspberry Jams all over the world to take place over the Raspberry Jam Big Birthday Weekend, 3-4 March 2018. A massive thank you to everyone who ran an event and attended.
The Raspberry Jam photo booth
I put together code for a Pi-powered photo booth which overlaid the Big Birthday Weekend logo onto photos and (optionally) tweeted them. We included an arcade button in the Jam kits so they could build one — and it seemed to be quite popular. Some Jams put great effort into housing their photo booth:
If you want to try out the photo booth software yourself, find the code on GitHub.
The great Raspberry Jam bake-off
Traditionally, in the UK, people have a cake on their birthday. And we had a few! We saw (and tasted) a great selection of Pi-themed cakes and other baked goods throughout the weekend:
Raspberry Jams everywhere
We always say that every Jam is different, but there’s a common and recognisable theme amongst them. It was great to see so many different venues around the world filling up with like-minded Pi enthusiasts, Raspberry Jam–branded banners, and Raspberry Pi balloons!
Thank you so much to all the attendees of the Ikana Jam in Krakow past Saturday! We shared fun experiences, some of them… also painful 😉 A big thank you to @Raspberry_Pi for these global celebrations! And a big thank you to @hubraum for their hospitality! #PiParty #rjam
Being one of the two places in Kenya where the #PiParty took place, it was an amazing time spending the day with this team and getting to learn and have fun. @TaitaTavetaUni and @Raspberry_Pi thank you for your support. @TTUTechlady @mictecttu ch
The Philly & Pi #PiParty event with @Bresslergroup and @TechGirlzorg was awesome! The Scratch and Pi workshop was amazing! It was overall a great day of fun and tech!!! Thank you everyone who came out!
Thanks everyone who came out to the @Raspberry_Pi Big Birthday Jam! Special thanks to @PBFerrell @estefanniegg @pcsforme @pandafulmanda @colnels @bquentin3 couldn’t’ve put on this amazing community event without you guys!
Personally, I managed to get to three Jams over the weekend: two run by the same people who put on the first two Jams to ever take place, and also one brand-new one! The Preston Raspberry Jam team, who usually run their event on a Monday evening, wanted to do something extra special for the birthday, so they came up with the idea of putting on a Raspberry Jam Sandwich — on the Friday and Monday around the weekend! This meant I was able to visit them on Friday, then attend the Manchester Raspberry Jam on Saturday, and finally drop by the new Jam at Worksop College on my way home on Sunday.
Thanks to everyone who came to our Jam and everyone who helped out. @phoenixtogether thanks for amazing cake & hosting. Ademir you’re so cool. It was awesome to meet Craig Morley from @Raspberry_Pi too. #PiParty
It’s @Raspberry_Pi 6th birthday and we’re celebrating by taking part in @amsterjam__! Happy Birthday Raspberry Pi, we’re so happy to be a part of the family! #PiParty
For more Jammy birthday goodness, check out the PiParty hashtag on Twitter!
The Jam makers!
A lot of preparation went into each Jam, and we really appreciate all the hard work the Jam makers put in to making these events happen, on the Big Birthday Weekend and all year round. Thanks also to all the teams that sent us a group photo:
Lots of the Jams that took place were brand-new events, so we hope to see them continue throughout 2018 and beyond, growing the Raspberry Pi community around the world and giving more people, particularly youths, the opportunity to learn digital making skills.
So many wonderful people in the @Raspberry_Pi community. Thanks to everyone at #PottonPiAndPints for a great afternoon and for everything you do to help young people learn digital making. #PiParty
Special thanks to ModMyPi for shipping the special Raspberry Jam kits all over the world!
Don’t forget to check out our Jam page to find an event near you! This is also where you can find free resources to help you get a new Jam started, and download free starter projects made especially for Jam activities. These projects are available in English, Français, Français Canadien, Nederlands, Deutsch, Italiano, and 日本語. If you’d like to help us translate more content into these and other languages, please get in touch!
PS Some of the UK Jams were postponed due to heavy snowfall, so you may find there’s a belated sixth-birthday Jam coming up where you live!
Big things are afoot in the world of HackSpace magazine! This month we’re running our first special issue, with wearables projects throughout the magazine. Moreover, we’re giving away our first subscription gift free to all 12-month print subscribers. Lastly, and most importantly, we’ve made the cover EXTRA SHINY!
Prepare your eyeballs — it’s HackSpace magazine issue 4!
In this issue, we’re taking an in-depth look at wearable tech. Not Fitbits or Apple Watches — we’re talking stuff you can make yourself, from projects that take a couple of hours to put together, to the huge, inspiring builds that are bringing technology to the runway. If you like wearing clothes and you like using your brain to make things better, then you’ll love this feature.
We’re continuing our obsession with Nixie tubes, with the brilliant Time-To-Go-Clock – Trump edition. This ingenious bit of kit uses obsolete Russian electronics to count down the time until the end of the 45th president’s term in office. However, you can also program it to tell the time left to any predictable event, such as the deadline for your tax return or essay submission, or the date England gets knocked out of the World Cup.
We’re also talking to Dr Lucy Rogers — NASA alumna, Robot Wars judge, and fellow of the Institution of Mechanical Engineers — about the difference between making as a hobby and as a job, and about why we need the Guild of Makers. Plus, issue 4 has a teeny boat, the most beautiful Raspberry Pi cases you’ve ever seen, and it explores the results of what happens when you put a bunch of hardware hackers together in a French chateau — sacré bleu!
As always, we’ve got more how-tos than you can shake a soldering iron at. Fittingly for the current climate here in the UK, there’s a hot water monitor, which shows you how long you have before your morning shower turns cold, and an Internet of Tea project to summon a cuppa from your kettle via the web. Perhaps not so fittingly, there’s also an ESP8266 project for monitoring a solar power station online. Readers in the southern hemisphere, we’ll leave that one for you — we haven’t seen the sun here for months!
And there’s more!
We’re super happy to say that all our 12-month print subscribers have been sent an Adafruit Circuit Playground Express with this new issue:
This gadget was developed primarily with wearables in mind and comes with all sorts of in-built functionality, so subscribers can get cracking with their latest wearable project today! If you’re not a 12-month print subscriber, you’ll miss out, so subscribe here to get your magazine and your device, and let us know what you’ll make.
Here at Backblaze we have a lot of folks who are all about technology. With the holiday season fast approaching, you might have all of your gift buying already finished — but if not, we put together a list of things that the employees here at Backblaze are pretty excited about giving (and/or receiving) this year.
It’s no secret that having a smart home is the new hotness, and many of the items below can be used to turbocharge your home’s ascent into the future:
Raspberry Pi The holidays are all about eating pie — well why not get a pie of a different type for the DIY fan in your life! Wyze Cam An inexpensive way to keep a close eye on all your favorite people…and intruders! Snooz Have trouble falling asleep? Try this portable white noise machine. Also great for the office! Amazon Echo Dot Need a cheap way to keep track of your schedule or play music? The Echo Dot is a great entry into the smart home of your dreams! Google Wifi These little fellows make it easy to Wifi-ify your entire home, even if it’s larger than the average shoe box here in Silicon Valley. Google Wifi acts as a mesh router and seamlessly covers your whole dwelling. Have a mansion? Buy more! Google Home Like the Amazon Echo Dot, this is the Google variant. It’s more expensive (similar to the Amazon Echo) but has better sound quality and is tied into the Google ecosystem. Nest Thermostat This is a smart thermostat. What better way to score points with the in-laws than installing one of these bad boys in their home — and then making it freezing cold randomly in the middle of winter from the comfort of your couch!
Homes aren’t the only things that should be smart. Your body should also get the chance to be all that it can be:
Apple AirPods You’ve seen these all over the place, and the truth is they do a pretty good job of making sounds appear in your ears. Bose SoundLink Wireless Headphones If you like over-the-ear headphones, these noise canceling ones work great, are wireless and lovely. There’s no better way to ignore people this holiday season! Garmin Fenix 5 Watch This watch is all about fitness. If you enjoy fitness. This watch is the fitness watch for your fitness needs. Apple Watch The Apple Watch is a wonderful gadget that will light up any movie theater this holiday season. Nokia Steel Health Watch If you’re into mixing analogue and digital, this is a pretty neat little gadget. Fossil Smart Watch This stylish watch is a pretty neat way to dip your toe into smartwatches and activity trackers. Pebble Time Steel Smart Watch Some people call this the greatest smartwatch of all time. Those people might be named Yev. This watch is great at sending you notifications from your phone, and not needing to be charged every day. Bellissimo!
A few of the holiday gift suggestions that we got were a bit off-kilter, but we do have a lot of interesting folks in the office. Hopefully, you might find some of these as interesting as they do:
Wireless Qi Charger Wireless chargers are pretty great in that you don’t have to deal with dongles. There are even kits to make your electronics “wirelessly chargeable” which is pretty great! Self-Heating Coffee Mug Love coffee? Hate lukewarm coffee? What if your coffee cup heated itself? Brilliant! Yeast Stirrer Yeast. It makes beer. And bread! Sometimes you need to stir it. What cooler way to stir your yeast than with this industrial stirrer? Toto Washlet This one is self explanatory. You know the old rhyme: happy butts, everyone’s happy!
Looking for the perfect Christmas gift for a beloved maker in your life? Maybe you’d like to give a relative or friend a taste of the world of coding and Raspberry Pi? Whatever you’re looking for, the Raspberry Pi Christmas shopping list will point you in the right direction.
For those getting started
Thinking about introducing someone special to the wonders of Raspberry Pi during the holidays? Although you can set up your Pi with peripherals from around your home, such as a mobile phone charger, your PC’s keyboard, and the old mouse dwelling in an office drawer, a starter kit is a nice all-in-one package for the budding coder.
If you’re looking for something for a confident digital maker, you can’t go wrong with adding to their arsenal of electric and electronic bits and bobs that are no doubt cluttering drawers and boxes throughout their house.
Components such as servomotors, displays, and sensors are staples of the maker world. And when it comes to jumper wires, buttons, and LEDs, one can never have enough.
You could also consider getting your person a soldering iron, some helpings hands, or small tools such as a Dremel or screwdriver set.
And to make their life a little less messy, pop it all inside a Really Useful Box…because they’re really useful.
For kit makers
While some people like to dive into making head-first and to build whatever comes to mind, others enjoy working with kits.
The Naturebytes kit allows you to record the animal visitors of your garden with the help of a camera and a motion sensor. Footage of your local badgers, birds, deer, and more will be saved to an SD card, or tweeted or emailed to you if it’s in range of WiFi.
Coretec’s Tiny 4WD is a kit for assembling a Pi Zero–powered remote-controlled robot at home. Not only is the robot adorable, building it also a great introduction to motors and wireless control.
Looking for something small to keep your loved ones occupied on Christmas morning? Or do you have to buy a Secret Santa gift for the office tech? Here are some wonderful stocking fillers to fill your boots with this season.
The Pi Hut 3D Xmas Tree: available as both a pre-soldered and a DIY version, this gadget will work with any 40-pin Raspberry Pi and allows you to create your own mini light show.
Google AIY Voice kit: build your own home assistant using a Raspberry Pi, the MagPi Essentials guide, and this brand-new kit. “Google, play Mariah Carey again…”
LEGO Idea’s bought out this amazing ‘Women of NASA’ set, and I thought it would be fun to build, play and learn from these inspiring women! First up, let’s discover a little more about Sally Ride and Mae Jemison, two AWESOME ASTRONAUTS!
Treat the kids, and big kids, in your life to the newest LEGO Ideas set, the Women of NASA — starring Nancy Grace Roman, Margaret Hamilton, Sally Ride, and Mae Jemison!
Explore the world of wearables with Pimoroni’s sewable, hackable, wearable, adorable Bearables kits.
With so many amazing kits, HATs, and books available from members of the Raspberry Pi community, it’s hard to only pick a few. Have you found something splendid for the maker in your life? Maybe you’ve created your own kit that uses the Raspberry Pi? Share your favourites with us in the comments below or via our social media accounts.
HackSpace magazine is finally here! Grab your copy of the new magazine for makers today, and try your hand at some new, exciting skills.
What is HackSpace magazine?
HackSpace magazine is the newest publication from the team behind The MagPi. Chock-full of amazing projects, tutorials, features, and maker interviews, HackSpace magazine brings together the makers of the world every month, with you — the community — providing the content.
The new magazine for the modern maker is out now! Learn more at https://hsmag.cc HackSpace magazine is the new monthly magazine for people who love to make things and those who want to learn. Grab some duct tape, fire up a microcontroller, ready a 3D printer and hack the world around you!
Inside issue 1
Fancy smoking bacon with your very own cold smoker? How about protecting your home with a mini trebuchet for your front lawn? Or maybe you’d like to learn from awesome creator Becky Stern how to get paid for making the things you love? No matter whether it’s handheld consoles, robot prosthetics, Christmas projects, or, er, duct tape — whatever your maker passion, issue 1 is guaranteed to tick your boxes!
HackSpace magazine is packed with content from every corner of the maker world: from welding to digital making, and from woodwork to wearables. And whatever you enjoy making, we want to see it! So as you read through this first issue, imagine your favourite homemade projects on our pages, then make that a reality by emailing us the details via [email protected].
Get your copy
You can grab issue 1 of HackSpace magazine right now from WHSmith, Tesco, Sainsbury’s, and independent newsagents. If you live in the US, check out your local Barnes & Noble, Fry’s, or Micro Center next week. We’re also shipping to stores in Australia, Hong Kong, Canada, Singapore, Belgium and Brazil — ask your local newsagent whether they’ll be getting HackSpace magazine. Alternatively, you can get the new issue online from our store, or digitally via our Android or iOS apps. And don’t forget, as with all our publications, a free PDF of HackSpace magazine is available from release day.
We’re also offering money-saving subscriptions — find details on the the magazine website. And if you’re a subscriber of The MagPi, your free copy of HackSpace magazine is on its way, with details of a super 50% discount on subscriptions! Could this be the Christmas gift you didn’t know you wanted?
Share your makes and thoughts
Make sure to follow HackSpace magazine on Facebook and Twitter, or email the team at [email protected] to tell us about your projects and share your thoughts about issue 1. We’ve loved creating this new magazine for the maker community, and we hope you enjoy it as much as we do.
This post courtesy of Aaron Friedman, Healthcare and Life Sciences Partner Solutions Architect, AWS and Angel Pizarro, Genomics and Life Sciences Senior Solutions Architect, AWS
Precision medicine is tailored to individuals based on quantitative signatures, including genomics, lifestyle, and environment. It is often considered to be the driving force behind the next wave of human health. Through new initiatives and technologies such as population-scale genomics sequencing and IoT-backed wearables, researchers and clinicians in both commercial and public sectors are gaining new, previously inaccessible insights.
Many of these precision medicine initiatives are already happening on AWS. A few of these include:
PrecisionFDA – This initiative is led by the US Food and Drug Administration. The goal is to define the next-generation standard of care for genomics in precision medicine.
Deloitte ConvergeHEALTH – Gives healthcare and life sciences organizations the ability to analyze their disparate datasets on a singular real world evidence platform.
Central to many of these initiatives is genomics, which gives healthcare organizations the ability to establish a baseline for longitudinal studies. Due to its wide applicability in precision medicine initiatives—from rare disease diagnosis to improving outcomes of clinical trials—genomics data is growing at a larger rate than Moore’s law across the globe. Many expect these datasets to grow to be in the range of tens of exabytes by 2025.
Genomics data is also regularly re-analyzed by the community as researchers develop new computational methods or compare older data with newer genome references. These trends are driving innovations in data analysis methods and algorithms to address the massive increase of computational requirements.
Edico Genome, an AWS Partner Network (APN) Partner, has developed a novel solution that accelerates genomics analysis using field-programmable gate arrays, or FPGAs. Historically, Edico Genome deployed their FPGA appliances on-premises. When AWS announced the Amazon EC2 F1 PGA-based instance family in December 2016, Edico Genome adopted a cloud-first strategy, became a F1 launch partner, and was one of the first partners to deploy FPGA-enabled applications on AWS.
On October 19, 2017, Edico Genome partnered with the Children’s Hospital of Philadelphia (CHOP) to demonstrate their FPGA-accelerated genomic pipeline software, called DRAGEN. It can significantly reduce time-to-insight for patient genomes, and analyzed 1,000 genomes from the Center for Applied Genomics Biobank in the shortest time possible. This set a Guinness World Record for the fastest analysis of 1000 whole human genomes, and they did this using 1000 EC2 f1.2xlarge instances in a single AWS region. Not only were they able to analyze genomes at high throughput, they did so averaging approximately $3 per whole human genome of AWS compute for the analysis.
The version of DRAGEN that Edico Genome used for this analysis was also the same one used in the precisionFDA Hidden Treasures – Warm Up challenge, where they were one of the top performers in every assessment.
In the remainder of this post, we walk through the architecture used by Edico Genome, combining EC2 F1 instances and AWS Batch to achieve this milestone.
EC2 F1 instances and Edico’s DRAGEN
EC2 F1 instances provide access to programmable hardware-acceleration using FPGAs at a cloud scale. AWS customers use F1 instances for a wide variety of applications, including big data, financial analytics and risk analysis, image and video processing, engineering simulations, AR/VR, and accelerated genomics. Edico Genome’s FPGA-backed DRAGEN Bio-IT Platform is now integrated with EC2 F1 instances. You can access the accuracy, speed, flexibility, and low compute cost of DRAGEN through a number of third-party platforms, AWS Marketplace, and Edico Genome’s own platform. The DRAGEN platform offers a scalable, accelerated, and cost-efficient secondary analysis solution for a wide variety of genomics applications. Edico Genome also provides a highly optimized mechanism for the efficient storage of genomic data.
Scaling DRAGEN on AWS
Edico Genome used 1,000 EC2 F1 instances to help their customer, the Children’s Hospital of Philadelphia (CHOP), to process and analyze all 1,000 whole human genomes in parallel. They used AWS Batch to provision compute resources and orchestrate DRAGEN compute jobs across the 1,000 EC2 F1 instances. This solution successfully addressed the challenge of creating a scalable genomic processing pipeline that can easily scale to thousands of engines running in parallel.
A simplified view of the architecture used for the analysis is shown in the following diagram:
DRAGEN’s portal uses Elastic Load Balancing and Auto Scaling groups to scale out EC2 instances that submitted jobs to AWS Batch.
Job metadata is stored in their Workflow Management (WFM) database, built on top of Amazon Aurora.
The DRAGEN Workflow Manager API submits jobs to AWS Batch.
These jobs are executed on the AWS Batch managed compute environment that was responsible for launching the EC2 F1 instances.
These jobs run as Docker containers that have the requisite DRAGEN binaries for whole genome analysis.
As each job runs, it retrieves and stores genomics data that is staged in Amazon S3.
The steps listed previously can also be bucketed into the following higher-level layers:
Workflow: Edico Genome used their Workflow Management API to orchestrate the submission of AWS Batch jobs. Metadata for the jobs (such as the S3 locations of the genomes, etc.) resides in the Workflow Management Database backed by Amazon Aurora.
Batch execution: AWS Batch launches EC2 F1 instances and coordinates the execution of DRAGEN jobs on these compute resources. AWS Batch enabled Edico to quickly and easily scale up to the full number of instances they needed as jobs were submitted. They also scaled back down as each job was completed, to optimize for both cost and performance.
Compute/job: Edico Genome stored their binaries in a Docker container that AWS Batch deployed onto each of the F1 instances, giving each instance the ability to run DRAGEN without the need to pre-install the core executables. The AWS based DRAGEN solution streams all genomics data from S3 for local computation and then writes the results to a destination bucket. They used an AWS Batch job role that specified the IAM permissions. The role ensured that DRAGEN only had access to the buckets or S3 key space it needed for the analysis. Jobs didn’t need to embed AWS credentials.
In the following sections, we dive deeper into several tasks that enabled Edico Genome’s scalable FPGA genome analysis on AWS:
Prepare your Amazon FPGA Image for AWS Batch
Create a Dockerfile and build your Docker image
Set up your AWS Batch FPGA compute environment
In brief, you need a modern Linux distribution (3.10+), Amazon ECS Container Agent, awslogs driver, and Docker configured on your image. There are additional recommendations in the Compute Resource AMI specification.
Preparing your Amazon FPGA Image for AWS Batch
You can use any Amazon Machine Image (AMI) or Amazon FPGA Image (AFI) with AWS Batch, provided that it meets the Compute Resource AMI specification. This gives you the ability to customize any workload by increasing the size of root or data volumes, adding instance stores, and connecting with the FPGA (F) and GPU (G and P) instance families.
Next, install the AWS CLI:
pip install awscli
Add any additional software required to interact with the FPGAs on the F1 instances.
As a starting point, AWS publishes an FPGA Developer AMI in the AWS Marketplace. It is based on a CentOS Linux image and includes pre-integrated FPGA development tools. It also includes the runtime tools required to develop and use custom FPGAs for hardware acceleration applications.
There are two common methods for connecting to AWS Batch to run FPGA-enabled algorithms. The first method, which is the route Edico Genome took, involves storing your binaries in the Docker container itself and running that on top of an F1 instance with Docker installed. The following code example is what a Dockerfile to build your container might look like for this scenario.
# DRAGEN_EXEC Docker image generator –
# Run this Dockerfile from a local directory that contains the latest release of
# - Dragen RPM and Linux DMA Driver available from Edico
# - Edico's Dragen WFMS Wrapper files
RUN rpm -Uvh https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
# Install Basic packages needed for Dragen
RUN yum -y install \
# Install the Dragen RPM
RUN mkdir -m777 -p /var/log/dragen /var/run/dragen
ADD . /root
RUN rpm -Uvh /root/edico_driver*.rpm || true
RUN rpm -Uvh /root/dragen-aws*.rpm || true
# Auto generate the Dragen license
RUN /opt/edico/bin/dragen_lic -i auto
# Now install the Edico WFMS "Wrapper" functions
# Add development tools needed for some util
RUN yum groupinstall -y "Development Tools"
# Install necessary standard packages
RUN yum -y install \
tree && \
pip install – upgrade pip && \
easy_install requests && \
pip install psutil && \
pip install python-dateutil && \
pip install constants && \
# Setup Python path used by the wrapper
RUN mkdir -p /opt/workflow/python/bin
RUN ln -s /usr/bin/python /opt/workflow/python/bin/python2.7
RUN ln -s /usr/bin/python /opt/workflow/python/bin/python
# Install d_haul and dragen_job_execute wrapper functions and associated packages
RUN mkdir -p /root/wfms/trunk/scheduler/scheduler
COPY scheduler/d_haul /root/wfms/trunk/scheduler/
COPY scheduler/dragen_job_execute /root/wfms/trunk/scheduler/
COPY scheduler/scheduler/aws_utils.py /root/wfms/trunk/scheduler/scheduler/
COPY scheduler/scheduler/constants.py /root/wfms/trunk/scheduler/scheduler/
COPY scheduler/scheduler/job_utils.py /root/wfms/trunk/scheduler/scheduler/
COPY scheduler/scheduler/logger.py /root/wfms/trunk/scheduler/scheduler/
COPY scheduler/scheduler/scheduler_utils.py /root/wfms/trunk/scheduler/scheduler/
COPY scheduler/scheduler/webapi.py /root/wfms/trunk/scheduler/scheduler/
COPY scheduler/scheduler/wfms_exception.py /root/wfms/trunk/scheduler/scheduler/
RUN touch /root/wfms/trunk/scheduler/scheduler/__init__.py
# Landing directory should be where DJX is located
# Debug print of container's directories
RUN tree /root/wfms/trunk/scheduler
# Default behaviour. Over-ride with – entrypoint on docker run cmd line
Note: Edico Genome’s custom Python wrapper functions for its Workflow Management System (WFMS) in the latter part of this Dockerfile should be replaced with functions that are specific to your workflow.
The second method is to install binaries and then use Docker as a lightweight connector between AWS Batch and the AFI. For example, this might be a route you would choose to use if you were provisioning DRAGEN from the AWS Marketplace.
In this case, the Dockerfile would not contain the installation of the binaries to run DRAGEN, but would contain any other packages necessary for job completion. When you run your Docker container, you enable Docker to access the underlying file system.
Connecting to AWS Batch
AWS Batch provisions compute resources and runs your jobs, choosing the right instance types based on your job requirements and scaling down resources as work is completed. AWS Batch users submit a job, based on a template or “job definition” to an AWS Batch job queue.
Job queues are mapped to one or more compute environments that describe the quantity and types of resources that AWS Batch can provision. In this case, Edico created a managed compute environment that was able to launch 1,000 EC2 F1 instances across multiple Availability Zones in us-east-1. As jobs are submitted to a job queue, the service launches the required quantity and types of instances that are needed. As instances become available, AWS Batch then runs each job within appropriately sized Docker containers.
The Edico Genome workflow manager API submits jobs to an AWS Batch job queue. This job queue maps to an AWS Batch managed compute environment containing On-Demand F1 instances. In this section, you can set this up yourself.
To create the compute environment that DRAGEN can use:
An f1.2xlarge EC2 instance contains one FPGA, eight vCPUs, and 122-GiB RAM. As DRAGEN requires an entire FPGA to run, Edico Genome needed to ensure that only one analysis per time executed on an instance. By using the f1.2xlarge vCPUs and memory as a proxy in their AWS Batch job definition, Edico Genome could ensure that only one job runs on an instance at a time. Here’s what that looks like in the AWS CLI:
You can query the status of your DRAGEN job with the following command:
aws batch describe-jobs – jobs <the job ID from the above command>
The logs for your job are written to the /aws/batch/job CloudWatch log group.
In this post, we demonstrated how to set up an environment with AWS Batch that can run DRAGEN on EC2 F1 instances at scale. If you followed the walkthrough, you’ve replicated much of the architecture Edico Genome used to set the Guinness World Record.
There are several ways in which you can harness the computational power of DRAGEN to analyze genomes at scale. First, DRAGEN is available through several different genomics platforms, such as the DNAnexus Platform. DRAGEN is also available on the AWS Marketplace. You can apply the architecture presented in this post to build a scalable solution that is both performant and cost-optimized.
For more information about how AWS Batch can facilitate genomics processing at scale, be sure to check out our aws-batch-genomics GitHub repo on high-throughput genomics on AWS.
OK, fine. You’re after something properly frightening. How about the haunted magic mirror by Kapitein Haak, or this one, with added Philips Hue effects, by Ben Eagan. As if your face first thing in the morning wasn’t shocking enough.
If you find those rigid-faced, bow-lipped, plastic dolls more sinister than sweet – and you’re right to do so: they’re horrible – you won’t like this evil toy. Possessed by an unquiet shade, it’s straight out of my nightmares.
Earlier this month we covered Adafruit’s haunted portrait how-to. This build by Dominick Marino takes that concept to new, terrifying, heights.
This recreation of Billy the Puppet from the Saw franchise is Pi-powered, it’s mobile, and it talks. You can remotely control it, and I am not even remotely OK with it. That being said, if you’re keen to have one of your own, be my guest. Just follow the guide on Instructables. It’s your funeral.
Make your Halloween
It’s been a great year for scary Raspberry Pi makes, and we hope you have a blast using your Pi to get into the Halloween spirit.
And speaking of spirits, Matt Reed of RedPepper has created a Pi-based ghost detector! It uses Google’s Speech Neural Network AI to listen for voices in the ether, and it’s live-streaming tonight. Perfect for watching while you’re waiting for the trick-or-treaters to show up.
Halloween: that glorious time of year when you’re officially allowed to make your friends jump out of their skin with your pranks. For those among us who enjoy dressing up, Halloween is also the occasion to go all out with costumes. And so, dear reader, we present to you: a steampunk tentacle hat, created by Derek Woodroffe.
Derek is an engineer who loves all things electronics. He’s part of Extreme Kits, and he runs the website Extreme Electronics. Raspberry Pi Zero-controlled Tesla coils are Derek’s speciality — he’s even been on one of the Royal Institution’s Christmas Lectures with them! Skip ahead to 15:06 in this video to see Derek in action:
The first Lecture from Professor Saiful Islam’s 2016 series of CHRISTMAS LECTURES, ‘Supercharged: Fuelling the future’. Watch all three Lectures here: http://richannel.org/christmas-lectures 2016 marked the 80th anniversary since the BBC first broadcast the Christmas Lectures on TV. To celebrate, chemist Professor Saiful Islam explores a subject that the lectures’ founder – Michael Faraday – addressed in the very first Christmas Lectures – energy.
Wearables are electronically augmented items you can wear. They might take the form of spy eyeglasses, clothes with integrated sensors, or, in this case, headgear adorned with mechanised tentacles.
Why did Derek make this? We’re not entirely sure, but we suspect he’s a fan of the Cthulu mythos. In any case, we were a little astounded by his project. This is how we reacted when Derek tweeted us about it:
@ExtElec @extkits This is beyond incredible and completely unexpected.
In fact, we had to recover from a fit of laughter before we actually managed to type this answer.
Making a steampunk tentacle hat
Derek made the ‘skeleton’ of each tentacle out of a net curtain spring, acrylic rings, and four lengths of fishing line. Two servomotors connect to two ends of fishing line each, and pull them to move the tentacle.
Then he covered the tentacles with nylon stockings and liquid latex, glued suckers cut out of MDF onto them, and mounted them on an acrylic base. The eight motors connect to a Raspberry Pi via an I2C 8-port PWM controller board.
The Pi makes the servos pull the tentacles so that they move in sine waves in both the x and y directions, seemingly of their own accord. Derek cut open the top of a hat to insert the mounted tentacles, and he used more liquid latex to give the whole thing a slimy-looking finish.
Iä! Iä! Cthulhu fhtagn!
You can read more about Derek’s steampunk tentacle hat here. He will be at the Beeston Raspberry Jam in November to show off his build, so if you’re in the Nottingham area, why not drop by?
Wearables for Halloween
This build is already pretty creepy, but just imagine it with a sensor- or camera-powered upgrade that makes the tentacles reach for people nearby. You’d have nightmare fodder for weeks.
With the help of the Raspberry Pi, any Halloween costume can be taken to the next level. How could Pi technology help you to win that coveted ‘Scariest costume’ prize this year? Tell us your ideas in the comments, and be sure to share pictures of you in your get-up with us on Twitter, Facebook, or Instagram.
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