openaps · scottleibrand · Jul 21, 2015 · Jul 12, 2015 · Jul 12, 2015 · Jul 12, 2015
diff --git a/Building-a-system/building.md b/Building-a-system/building.md
@@ -0,0 +1,34 @@
+# Building an OpenAPS Implementation
+
+This section describes how to go from using the openaps tools in isolation to building your own OpenAPS implementation. For a number or reasons, this document can neither provide explicit instructions on how to construct a functional artificial pancreas nor recommend that you use the openaps tools for dosing insulin. What can be provided is an approach that can help guide this transition through a series of phases. 
+
+In each phase, look to accomplish a set of goals relating to the functionality of your system as well as gain some further abilities to contribute back to the OpenAPS community. Five phases:
+
+
+* [Phase 0: Initial Setup](Building-a-system/initial-setup.md)<br>
+Acquire and configuring hardware, install software, and become familiar with the openaps environment
+
+* [Phase 1: Data Collection](Building-a-system/data-collection.md)<br>
+Build a system for logging and analyzing pump and CGM data
+
+* [Phase 2: Recommendation Engine](Building-a-system/recommendation-engine.md)<br>
+Use the logged data to suggest insulin dosage adjustment, review and refine algorithms, test different scenarios for safety
+
+* [Phase 3: Closing the Loop](Building-a-system/closing-the-loop.md)<br>
+Apply the recommendations, automatically and in real time
+
+* [Phase 4: Getting Fancy](Building-a-system/getting-fancy.md)<br>
+Improve the functionality of the implementation with additional software or hardware development
+
+The document subsection for each phase has three components outlined:
+* Upon Completion<br>
+The capabilities that the user and system should have after completing the phase  
+
+* Phase Tasks<br>
+Tasks or steps to take during the phase
+
+* Community Contribution
+Ways that a user should be able to contribute to the #OpenAPS project and/or openaps tool set during and after the phase
+
+These phase descriptions are purely suggestive and are by no means a required method for building an OpenAPS implementation. They serve as one possible path to step through the development process in a structured way.
+
diff --git a/Building-a-system/closing-the-loop.md b/Building-a-system/closing-the-loop.md
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+# Phase 3: Closing the Loop
diff --git a/Building-a-system/data-collection.md b/Building-a-system/data-collection.md
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+# Phase 1: Data Collection
+Phase 1 focuses on accessing, logging, cleaning up, and analyzing data from the pump and CGM. Data fidelity is extremely important, especially when dosing is being considered. Take the time to review what the openaps tools are outputting and compare the logs against your own CareLink and CGM reports.
+
+* Upon Completion
+    * Be able to download, record, and recall data logs from pump and CGM
+    * Be able to download “real time” data
+    * Have data being sent via wireless connection to a cloud database for user access
+    * Have built a system able to collect data and be able to help others do the same
+
+
+* Phase Tasks
+    * Use tools to download data from pump and CGM
+    * Log data for future analysis, use in algorithms
+    * Ensure fidelity and accuracy of recorded readings
+    * Test edge cases
+    * Log data “in real time” to test hardware functionality
+    * Set up cloud database to accept uploaded data (optional)
+    * Have logged data syncing to cloud database (optional)
+
+
+* Community Contribution
+    * Provide feedback on ...
+        * Model-specific data issues (e.g. Medtronic 722 v 723)
+        * Using software tools
+        * Following guides to accomplish above phase tasks
+    * Help edit instructions for Phase 1
+    * Provide improved or alternative implementations
diff --git a/Building-a-system/getting-fancy.md b/Building-a-system/getting-fancy.md
@@ -0,0 +1,13 @@
+# Phase 4: Getting Fancy
+
+... also known as "gilding the lily" or "all the awesome stuff that everyone dreams of" or "the modifications that are required before you'd really want to show off your APS". These efforts are certainly worthwhile and bring out the best in technological creativity, but they also tend to distract in the early stages of development. 
+
+Some examples include:
+
+* Data visualization
+* Smartphone integration
+* On-board displays
+* Hardware size reduction
+* Hardware power consumption reduction
+* Refined analytical modeling
+* Integration with fitness trackers
diff --git a/Building-a-system/initial-setup.md b/Building-a-system/initial-setup.md
@@ -0,0 +1,22 @@
+# Phase 0: Initial Setup
+
+Phase 0 focuses on getting everything required for an OpenAPS implementation procured, installed, and ready for tinkering. This is primarily accomplished through following steps in the [Hardware](../Hardware/hardware.md) and [Setup](../Setup/setup.md) sections.  
+
+
+* Upon Completion
+    * Possess hardware and software tools necessary to build an OpenAPS implementation
+    * Have gone through the setup process and be able to help others do the same
+
+
+* Phase Tasks
+    * Procure hardware
+    * Download and install software and tools
+    * Test a subset of tools to make sure they work as expected
+
+
+* Community Contribution
+    * Provide feedback on ...
+        * Hardware procurement (cheap deals, alternatives)
+        * Difficulties with installation process (‘this looked different on my system” or “I couldn’t locate that menu” or “I ran into this error”)
+        * Solutions to overcome setup difficulties, especially for systems that are not yet covered (some different flavor of Linux, for example)
+    * Help edit setup instructions for accuracy, coverage, ease of understanding
diff --git a/Building-a-system/recommendation-engine.md b/Building-a-system/recommendation-engine.md
@@ -0,0 +1,29 @@
+# Phase 2: Recommendation Engine
+
+Phase 2 focuses on developing a suitable algorithm to recommend changes to insulin dosages. This is essentially a practice closed-loop system, with you completing the loop. This can be performed in real time or by using historical data and making retroactive suggestions. Pay special attention to situations where CGM readings are not smooth or there are issues with data connectivity or fidelity.
+
+If you haven't already done so, this is also an excellent time to calibrate your inputs, such as insulin sensitivity factor (ISF), carbohydrate ratio (CR), basal rates, et cetera.
+
+* Upon Completion
+    * Have a set of algorithms designed to control blood glucose via temp basals
+    * Have patient-specific inputs required for these algorithms
+    * Have those algorithms coded so as to take the data collection built in Phase 1 as input
+    * Have the code output recommendations as to how it would change temp basal rates
+    * Have the ability to utilize code on real-time and historical data to evaluate efficacy
+    * Have implemented, tested, and tuned one or more set of algorithms and be able to help others do the same
+
+
+* Phase Tasks
+    * Research the different strategies for single-hormone closed loop systems
+    * Complete relevant patient-specific studies to determine key inputs (e.g. carb absorption)
+    * Code one or more of these strategies such that they can accept live and/or historic patient data and output suggestions for temp basal changes
+    * Evaluate the efficacy of these algorithms by testing their suggestions against live and historic data
+    * Iterate on the algorithms and their implementation to improve their output
+    * Test cases of data corruption, lack of data, lack of connectivity, and other non-ideal operating conditions
+
+
+* Community Contributions
+    * Provide feedback on ...
+    * Help edit instructions for Phase 2
+    * Provide results of testing for comparing and contrasting with others
+    * Summarize research findings and synthesize them into jump-off points for others' research
diff --git a/Glossary/glossary.md b/Glossary/glossary.md
@@ -0,0 +1,24 @@
+# Glossary
+
+IOB
+
+DIA
+
+\#OpenAPS
+
+OpenAPS
+
+openaps
+
+CR
+
+ISF
+
+Bolus
+
+Basal
+
+APS
+
+CGM
+
diff --git a/Hardware/hardware.md b/Hardware/hardware.md
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+
+# Hardware
+This section describes the hardware components required for a 'typical' OpenAPS implementation. There are numerous variations and substitutions that can be made, but the following items are recommended for getting started. If you come across something that doesn't seem to work, is no longer available, or have a notable alternative, feel free to edit this document with your suggestions.
+
+
+## Recommended Hardware
+
+Required
+* Raspberry Pi 2 Model B
+* 8 GB (or greater) micro SD card
+* Low-profile USB WiFi adapter
+* 2.1 Amp (or greater) USB power supply
+* Medtronic CareLink USB stick
+* Medtronic insulin pump: 512/712, 515/715, 522/722, or 523/723 (with firmware 2.4A or lower) 
+* Dexcom CGM (G4 Platinum or Platinum with Share system) OR Medtronic CGM (MiniMed Paradigm REAL-Time Revel or Enlite)
+* Micro USB cable(s)
+
+Optional
+* Battery with USB output
+* Cat5 or Cat6 ethernet cable
+* HDMI cable
+
+A mostly complete kit recommended by several #OpenAPS contributors can be purchased through [Amazon](http://www.amazon.com/CanaKit-Raspberry-Complete-Original-Preloaded/dp/B008XVAVAW/ref=sr_1_1?ie=UTF8&qid=1434523139&sr=8-1&keywords=canakit+raspberry+pi+2). This kit has the RPi2, SD card, WiFi adapter, and wall power supply. It also comes with a case, HDMI cable, and heat sink, none of which are required for an OpenAPS build. The kit does not have a micros USB cable (required to connect a Dexcom G4 receiver to the RPi) or a battery, which can be used in lieu of the wall power supply for portability.
+
+Additionally, for the Raspberry Pi and peripherals, verified sets of working hardware can be found [here](http://elinux.org/RPi_VerifiedPeripherals).
+
+Eventually, once you have an entire OpenAPS build up and running, it is recommended that you have backup sets of equipment in case of failure.
+
+## Hardware Details & Recommendations
+
+**Raspberry Pi 2 Model B**
+
+The Raspberry Pi 2 (RPi2) model B is a credit-card sized single-board computer. The RPi2 primarily uses Linux kernel based operating systems, which must be installed by the user onto a micro SD card for the RPi2 to work. The RPi2 currently only supports Ubuntu, Raspbian, OpenELEC, and RISC OS. We recommend installing either Ubuntu or Raspbian. In this tutorial, you will learn how to do a "cableless" and "headless" install of Raspbian. You will be able to access and control the RPi2 via an SSH client on Windows, Mac OS X, Linux, iOS, or Android.
+
+The RPi2 has 4 USB ports, an ethernet port, an HDMI port, and a micro USB power-in jack that accepts 2.1 Amp power supplies. In this tutorial, you will need to access the USB ports, micro USB power-in jack, and possibly the Ethernet jack (if wireless failure occurs). You will not require the HDMI port or a monitor.
+
+[Raspberry Pi 2 Model B](https://www.raspberrypi.org/products/raspberry-pi-2-model-b/)
+
+<br>
+**Micro SD Card**
+
+An 8 or 16 GB micro SDHC card is recommended. Get one that is class-4 or greater and is a recognized name brand, such as SanDisk, Kingston, or Sony. A list of verified working hardware (including SD cards) can be found [here](http://elinux.org/RPi_VerifiedPeripherals).
+
+[Sony 16GB Class 10 UHS-1 Micro SDHC](http://www.amazon.com/Sony-Class-Memory-SR16UY2A-TQ/dp/B00X1404P8/ref=dp_ob_title_ce)
+
+<br>
+**WiFi Adapter**
+
+A minimalistic, unobtrusive WiFi USB adapter is recommended. The low-profile helps to avoid damage to both the RPi2 and the adapter as the RPi2 will be transported everywhere with the patient.
+
+[Buffalo AirStation N150 Wireless USB Adapter](http://www.amazon.com/BUFFALO-AirStation-N150-Wireless-Adapter/dp/B003ZM17RA/ref=sr_1_1?ie=UTF8&qid=1434523524&sr=8-1&keywords=airstation+n150)
+
+[Edimax EW-7811Un 150Mbps 11n Wi-Fi USB Adapter](http://www.amazon.com/Edimax-EW-7811Un-150Mbps-Raspberry-Supports/dp/B003MTTJOY/ref=sr_1_1?ie=UTF8&qid=1432614150&sr=8-1&keywords=edimax)
+
+<br>
+**2.1 Amp USB Battery Power Supply**
+
+A large-capacity power supply that is greater than 8000 mAh (milliAmp-hours) is recommended for full day use. Make sure that the battery has at least one 2.1 Amp USB output. A battery with a form-factor that minimizes size is recommended, to allow the patient to be as ambulatory as possible. When you have a full #OpenAPS system implemented and working, you will want to have multiple batteries to rotate and recharge.
+
+ [Power Bank 12000mAh Vinsic Genius External Mobile Battery Charger Pack](http://www.amazon.com/dp/B00M6V0R2C/ref=wl_it_dp_o_pC_nS_ttl?_encoding=UTF8&colid=2OYKR43UGE0YB&coliid=IC4EHVFRTC117&psc=1)
+
+ [Anker 2nd Gen Astro E3 Ultra Compact 10000mAh External Battery](http://www.amazon.com/gp/product/B009USAJCC/ref=od_aui_detailpages00?ie=UTF8&psc=1)
+
+<br>
+**CareLink USB Stick**
+
+Currently, the only supported device for uploading pump data and interfacing on the #OpenAPS is the CareLink USB stick. We recommend you purchase at least two sticks because if one breaks, acquiring another stick will take time and will delay development. Additionally, due to the short range of communication between the CareLink stick and the Medtronic pumps, some users set up multiple sticks in different locations to maximize the chances of successful transmissions.
+
+[Medtronic](https://medtronicdiabetes.secure.force.com/store/carelink-usb--remotes/usb-wireless-upload-device)
+
+ [American Diabetes Wholesale](http://www.adwdiabetes.com/product/minimed-carelink-usb-upload_1164.htm)
+
+<br>
+**CGM: Dexcom G4 Platinum System (with or without Share) OR Medtronic **
+
+The openaps tool set supports two different CGM systems: the Dexcom G4 Platinum system (with or without the Share functionality) and the Medtronic system. With Dexcom, the Share platform is not required as communication with the receiver is accomplished via USB. The Medtronic CGM system communicates directly with its associated pump, so the data can be retrieved using the CareLink USB stick.
+
+[Dexcom G4 Platinum with  Share](http://www.dexcom.com/dexcom-g4-platinum-share)
+
+[Medtronic Enlite](https://www.medtronicdiabetes.com/treatment-and-products/enlite-sensor)
+
+<br>
+**Medtronic Insulin Pump: 512/712, 515/715, 522/722, or 523/723 (with firmware 2.4A or lower)**
+
+Due to changes in the firmware, the openaps tools are only able to function in full on the above pump models. Security features were added in firmware version 2.5A that prevent making some remote adjustments via the CareLink USB stick. Each pump series is slightly different, and openaps functionality is still being ironed out for some of them. If you need to acquire an appropriate pump, check CraigsList or put out a request on [Gitter]( https://gitter.im/nightscout/intend-to-bolus) or the [#OpenAPS Google Group](https://groups.google.com/d/forum/openaps-dev). 
+
+There are several #OpenAPS participants working on ways to use other pumps (including non-Medtronic models). If you would like to get more information on the progress in these areas, take a look at the [#OpenAPS Google Group](https://groups.google.com/d/forum/openaps-dev).
+
+<br>
+**USB Cables**
+
+USB cables with a micro connector on one end and a standard (Type A) connector on the other are used to connect the power supply and the Dexcom receiver to the RPi2. Most cables will work fine, so but some prefer to select lengths and/or features (such as right-angled connectors) to improve portability.
+
+[Rerii Black Golden Plated 15 cm Length Micro-B Male Left Angle USB cable](http://www.amazon.com/Rerii-Micro-B-Charging-Guarantee-Fulfilled/dp/B00S9WXY5O/ref=sr_1_8?ie=UTF8&qid=1434603920&sr=8-8&keywords=micro+usb+right+angle)
+
+[Monoprice Premium USB to Micro USB Charge, Sync Cable - 3ft](http://www.monoprice.com/Product?c_id=103&cp_id=10303&cs_id=1030307&p_id=9763&seq=1&format=2)
diff --git a/Other-projects/aps-and-data-tools.md b/Other-projects/aps-and-data-tools.md
@@ -0,0 +1,17 @@
+## APS & Diabetes Data Tools
+
+* **\#DIYPS** (http://diyps.org/)
+
+* **simPancreas** (http://bustavo.com/category/simpancreas/)
+
+* **NightScout** (http://www.nightscout.info/)
+
+* **xDrip** (http://stephenblackwasalreadytaken.github.io/xDrip/)
+
+* **RileyLink** (https://github.com/ps2/rileylink)<br>
+A custom designed Bluetooth Smart (BLE) to 916MHz module. It can be used to bridge any BLE capable smartphone to the world of 916Mhz based devices. This project is focused on talking to Medtronic insulin pumps and sensors.
+
+* **Tidepool** (http://tidepool.org/)<br>
+Notably, work on Boston University iLet UI (https://github.com/tidepool-org/bionicpancreas)
+
+* **Perceptus** (http://perceptus.org)
diff --git a/Other-projects/commercial.md b/Other-projects/commercial.md
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+# Commercial APS Efforts
+
+There are currently several commercial closed-loop products in development by old and new companies in the diabetes treatment space. These include:
+
+* [Medtronic MiniMed 640G](https://www.medtronic-diabetes.com.au/insulin-pumps/640g)
+* [Medtronic MiniMed 670G](http://diatribe.org/drugdevice-name/medtronic-minimed-670g)
+* [TypeZero Technologies](http://www.typezero.com/)
+* [Bigfoot Biomedical](http://www.bigfootbiomedical.com/)
+* [Boston University's iLet](http://sites.bu.edu/bionicpancreas/)
diff --git a/Other-projects/other-projects.md b/Other-projects/other-projects.md
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+# Other Projects & Tools
+
+The following subsections provide links to other related projects as well as commercial artificial pancreas work underway.
diff --git a/Overview/closed-loop.md b/Overview/closed-loop.md
@@ -0,0 +1,8 @@
+#What is Closed Loop? 
+
+In general, a "closed loop" system for treatment of Diabetes is one in which insulin dosing—and in some cases glucagon dosing—is partially or completely automated. This is in contrast to an "open loop" system, where the user evaluates the inputs and manually instructs the insulin pump to dose a specific amount. In both cases, the goal is to maintain blood glucose within the desired range through adjusting hormone doses.
+
+There are numerous different types of closed loop systems, ranging from simple basal suspend systems designed to mitigate extreme hypoglycemia to dual hormone, fully automated systems. The JDRF (formerly Juvenile Diabetes Research Foundation) [Artificial Pancreas Project Plan](http://jdrf.org/research/treat/artificial-pancreas-project/) page provides an overview of the current commercial and academic generation-based approach. Several commercial systems are currently in development; see the [Commercial APS Efforts](Other-projects/commercial.md) for more information.
+
+
+While the openaps tools do not limit a user, \#OpenAPS is focused on a single-hormone hybrid closed-loop system—that is, one that uses only insulin (no glucagon) and does not aim to replace user interaction for mealtime bolusing. A primer on the theory of operation for #OpenAPS can be found at the [\#OpenAPS Reference Design](http://openaps.org/open-artificial-pancreas-system-openaps-reference-design/) page.
diff --git a/Overview/communication.md b/Overview/communication.md
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+# Communication Channels
+
+There are several ways to communicate with other participants and contributors in the #OpenAPS project.
+
+**Gitter**<br> 
+[Gitter](https://gitter.im/) is a messaging/chat service similar to IRC. It provides integration with GitHub and several other services. The [nightscout/intend-to-bolus]( https://gitter.im/nightscout/intend-to-bolus) channel is where you will find active #OpenAPS discussions ranging from technical issues with openaps tools to control theory to general pumping banter. It is a great place to introduce yourself and get some help from those who are a few steps further down the road.
+
+**Google Groups**<br>
+A private google group focused on #OpenAPS development work can be found [here](https://groups.google.com/d/forum/openaps-dev). Request access to participate and see some of the archived discussions.
+
+**Issues on openaps GitHub**<br> For reporting issues on the openaps tools fomrally, the openaps [issues page](https://github.com/openaps/openaps/issues) on GitHub is the proper forum. Feel free to try and get through the issues by working with others on the Gitter channel first if you think it may be something unrelated to the codebase.
+
+See also the [Resources](../Resources/resources.md) section for additional assistance.
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		# Other Projects & Tools

		The following subsections provide links to other related projects as well as commercial artificial pancreas work underway.