# eVOLVER

## eVOLVER

- [eVOLVER Documentation Wiki](https://khalil-lab.gitbook.io/evolver/evolver-documentation-wiki.md): Welcome to the eVOLVER documentation wiki! This aims to be a resource for all things eVOLVER, covering how to set up, use, modify, and troubleshoot hardware, software, and wetware on the platform.
- [About Us](https://khalil-lab.gitbook.io/evolver/general/about-us.md)
- [eVOLVER Community](https://khalil-lab.gitbook.io/evolver/general/evolver-community.md)
- [Code of Conduct](https://khalil-lab.gitbook.io/evolver/general/evolver-community/code-of-conduct.md)
- [Buying eVOLVER](https://khalil-lab.gitbook.io/evolver/getting-started/buying-evolver.md)
- [Part Sourcing](https://khalil-lab.gitbook.io/evolver/getting-started/part-sourcing.md)
- [Unboxing and Setting Up](https://khalil-lab.gitbook.io/evolver/getting-started/unboxing-and-setting-up.md)
- [Software Installation](https://khalil-lab.gitbook.io/evolver/getting-started/software-installation.md)
- [DPU Installation](https://khalil-lab.gitbook.io/evolver/getting-started/software-installation/dpu-installation.md): Process for installation of the Data Processing Unit (DPU)
- [Electron App (GUI) Installation](https://khalil-lab.gitbook.io/evolver/getting-started/software-installation/electron-app-gui-installation.md): Process for installing the Electron App (GUI) for eVOLVER.
- [Configuring Computer and Networking](https://khalil-lab.gitbook.io/evolver/getting-started/configuring-computer-and-networking.md): How to set up your computer to communicate with and run eVOLVER software.
- [Router Setup](https://khalil-lab.gitbook.io/evolver/getting-started/configuring-computer-and-networking/router-setup.md)
- [Calibrations](https://khalil-lab.gitbook.io/evolver/getting-started/calibrations.md)
- [Temperature Calibration](https://khalil-lab.gitbook.io/evolver/getting-started/calibrations/temperature-calibration.md): The goal of this tutorial is to learn how to calibrate the temperature settings for each Smart Sleeve in a 16 vial eVOLVER setup
- [Optical Density Calibration](https://khalil-lab.gitbook.io/evolver/getting-started/calibrations/optical-density-calibration.md): The goal of this tutorial is to learn how to efficiently generate OD calibration curves for each Smart Sleeve in a 16 vial eVOLVER setup.
- [Pump Calibration](https://khalil-lab.gitbook.io/evolver/getting-started/calibrations/pump-calibration.md)
- [Manual Calibration - calibrate.py](https://khalil-lab.gitbook.io/evolver/getting-started/calibrations/manual-calibration-calibrate.py.md)
- [Upgrade Base eVOLVER Hardware](https://khalil-lab.gitbook.io/evolver/upgrade-base-evolver-hardware.md)
- [Starting an Experiment](https://khalil-lab.gitbook.io/evolver/experiments/starting-an-experiment.md): List of things to do to setup and run an eVOLVER experiment.
- [Carboy Media Prep](https://khalil-lab.gitbook.io/evolver/experiments/starting-an-experiment/carboy-media-prep.md): Considerations while preparing large volumes of media for continuous culture in 20L carboys.
- [Preparing Vials](https://khalil-lab.gitbook.io/evolver/experiments/starting-an-experiment/preparing-vials.md)
- [Setup Waste Carboy](https://khalil-lab.gitbook.io/evolver/experiments/starting-an-experiment/setup-waste-carboy.md)
- [Sterilizing Lines](https://khalil-lab.gitbook.io/evolver/experiments/starting-an-experiment/sterilizing-lines.md)
- [Loading Vials and Setting Initial Conditions](https://khalil-lab.gitbook.io/evolver/experiments/starting-an-experiment/loading-vials-and-setting-initial-conditions.md)
- [OD Blank](https://khalil-lab.gitbook.io/evolver/experiments/starting-an-experiment/od-blank.md)
- [GUI Start Guide](https://khalil-lab.gitbook.io/evolver/experiments/starting-an-experiment/gui-start-guide.md): Guide for using the eVOLVER GUI to start and manage an experiment
- [Command Line Start Guide](https://khalil-lab.gitbook.io/evolver/experiments/starting-an-experiment/command-line-start-guide.md)
- [Cleaning Up After Experiment](https://khalil-lab.gitbook.io/evolver/experiments/starting-an-experiment/cleaning-up-after-experiment.md)
- [Growth Curve](https://khalil-lab.gitbook.io/evolver/experiments/growth-curve.md): Process and considerations for running a growth curve.
- [Chemostat](https://khalil-lab.gitbook.io/evolver/experiments/chemostat.md): Process and considerations for running a chemostat.
- [Turbidostat](https://khalil-lab.gitbook.io/evolver/experiments/turbidostat.md): Turbidostats are automated culturing systems used to maintain a constant cell density in microbial cultures.
- [FAQs](https://khalil-lab.gitbook.io/evolver/experiments/faqs.md)
- [Tips and Tricks](https://khalil-lab.gitbook.io/evolver/experiments/tips-and-tricks.md)
- [Use the GUI to Control Parameters](https://khalil-lab.gitbook.io/evolver/guides/use-the-gui-to-control-parameters.md): A guide for usage of the eVOLVER GUI to set parameters
- [Building a Smart Sleeve](https://khalil-lab.gitbook.io/evolver/guides/building-a-smart-sleeve.md): A guide for building Smart Sleeves on eVOLVER
- [Making media bottles and splitters](https://khalil-lab.gitbook.io/evolver/guides/making-media-bottles-and-splitters.md): For routing media from standard lab glassware
- [Emergency Efflux](https://khalil-lab.gitbook.io/evolver/guides/emergency-efflux.md)
- [Soldering Basics](https://khalil-lab.gitbook.io/evolver/guides/soldering-basics.md)
- [View the Server Log and Restart Server](https://khalil-lab.gitbook.io/evolver/guides/view-the-server-log-and-restart-server.md)
- [Updating the eVOLVER Server](https://khalil-lab.gitbook.io/evolver/guides/updating-the-evolver-server.md): Process for updating code on the eVOLVER Server (Raspberry Pi)
- [Change Your conf.yml File](https://khalil-lab.gitbook.io/evolver/guides/change-your-conf.yml-file.md)
- [Arduino Software Installation](https://khalil-lab.gitbook.io/evolver/guides/arduino-software-installation.md): Process for installing the Arduino IDE and necessary eVOLVER Arduino libraries.
- [Raspberry Pi Configuration](https://khalil-lab.gitbook.io/evolver/guides/raspberry-pi-configuration.md): Process for configuring a Raspberry Pi for eVOLVER
- [Command Line Usage](https://khalil-lab.gitbook.io/evolver/guides/command-line-usage.md): A guide to basic command line terminal usage on a UNIX based machine.
- [Millifluidics Guides](https://khalil-lab.gitbook.io/evolver/guides/millifluidics-guides.md)
- [Designing Millifluidics Using Eagle](https://khalil-lab.gitbook.io/evolver/guides/millifluidics-guides/designing-millifluidics-using-eagle.md)
- [Constructing Laser Cut Millifluidics](https://khalil-lab.gitbook.io/evolver/guides/millifluidics-guides/constructing-laser-cut-millifluidics.md)
- [Constructing Millifluidics via SLA Printing](https://khalil-lab.gitbook.io/evolver/guides/millifluidics-guides/constructing-millifluidics-via-sla-printing.md)
- [Calibrating IPPs](https://khalil-lab.gitbook.io/evolver/guides/millifluidics-guides/calibrating-ipps.md)
- [Operating Millifluidics](https://khalil-lab.gitbook.io/evolver/guides/millifluidics-guides/operating-millifluidics.md)
- [Troubleshooting Overview](https://khalil-lab.gitbook.io/evolver/troubleshooting/troubleshooting-overview.md)
- [Experiment Troubleshooting](https://khalil-lab.gitbook.io/evolver/troubleshooting/experiment-troubleshooting.md)
- [Contamination](https://khalil-lab.gitbook.io/evolver/troubleshooting/experiment-troubleshooting/contamination.md)
- [Vial Overflow, Pump Failure, and Spills](https://khalil-lab.gitbook.io/evolver/troubleshooting/experiment-troubleshooting/vial-overflow-pump-failure-and-spills.md)
- [Tubing and Connector Blockage and Bursting](https://khalil-lab.gitbook.io/evolver/troubleshooting/experiment-troubleshooting/tubing-and-connector-blockage-and-bursting.md)
- [Optical Density (OD) Readings](https://khalil-lab.gitbook.io/evolver/troubleshooting/optical-density-od-readings.md)
- [Vial Troubleshooting](https://khalil-lab.gitbook.io/evolver/troubleshooting/vial-troubleshooting.md)
- [Replacing Photodiodes and LEDs](https://khalil-lab.gitbook.io/evolver/troubleshooting/vial-troubleshooting/replacing-photodiodes-and-leds.md)
- [Heating Element](https://khalil-lab.gitbook.io/evolver/troubleshooting/vial-troubleshooting/heating-element.md)
- [Stirring](https://khalil-lab.gitbook.io/evolver/troubleshooting/vial-troubleshooting/stirring.md)
- [Server Troubleshooting](https://khalil-lab.gitbook.io/evolver/troubleshooting/server-troubleshooting.md)
- [Vial Platform Troubleshooting](https://khalil-lab.gitbook.io/evolver/troubleshooting/vial-platform-troubleshooting.md)
- [Motherboard Troubleshooting/Replacement](https://khalil-lab.gitbook.io/evolver/troubleshooting/vial-platform-troubleshooting/motherboard-troubleshooting-replacement.md)
- [12V Power Supply Troubleshooting/Replacement](https://khalil-lab.gitbook.io/evolver/troubleshooting/vial-platform-troubleshooting/12v-power-supply-troubleshooting-replacement.md)
- [GUI Troubleshooting](https://khalil-lab.gitbook.io/evolver/troubleshooting/gui-troubleshooting.md)
- [eVOLVER Maintenance](https://khalil-lab.gitbook.io/evolver/troubleshooting/evolver-maintenance.md)
- [Overview of Hardware Architecture](https://khalil-lab.gitbook.io/evolver/hardware/overview-of-hardware-architecture.md): High-level description of hardware architecture
- [Overview of Fluidics](https://khalil-lab.gitbook.io/evolver/hardware/overview-of-fluidics.md): Making culture continuous
- [Tubing and connectors](https://khalil-lab.gitbook.io/evolver/hardware/overview-of-fluidics/tubing-and-connectors.md): Also known as plumbing
- [Peristaltic Pumps](https://khalil-lab.gitbook.io/evolver/hardware/overview-of-fluidics/peristaltic-pumps.md): Just like the digestive system!
- [Fluidics box](https://khalil-lab.gitbook.io/evolver/hardware/overview-of-fluidics/fluidics-box.md): Separating fluidic control from the motherboard
- [Overview of Millifluidics](https://khalil-lab.gitbook.io/evolver/hardware/overview-of-millifluidics.md)
- [IPPs (Integrated Peristaltic Pumps)](https://khalil-lab.gitbook.io/evolver/hardware/overview-of-millifluidics/ipps-integrated-peristaltic-pumps.md)
- [Pressure Regulator](https://khalil-lab.gitbook.io/evolver/hardware/overview-of-millifluidics/pressure-regulator.md): Described initially in Huang, Heins et al. 2022 Nature Biotech
- [Vial Caps](https://khalil-lab.gitbook.io/evolver/hardware/vial-caps.md)
- [Universal Vial Cap Construction Guide (Luer Connectors Only)](https://khalil-lab.gitbook.io/evolver/hardware/vial-caps/universal-vial-cap-construction-guide-luer-connectors-only.md)
- [5 and 7 Port Nylon Tubing Caps Construction Protocol](https://khalil-lab.gitbook.io/evolver/hardware/vial-caps/5-and-7-port-nylon-tubing-caps-construction-protocol.md)
- [Smart Sleeve](https://khalil-lab.gitbook.io/evolver/hardware/smart-sleeve.md)
- [Vial Board](https://khalil-lab.gitbook.io/evolver/hardware/smart-sleeve/vial-board.md)
- [Stirring](https://khalil-lab.gitbook.io/evolver/hardware/smart-sleeve/stirring.md)
- [Temperature](https://khalil-lab.gitbook.io/evolver/hardware/smart-sleeve/temperature.md)
- [Optical Density](https://khalil-lab.gitbook.io/evolver/hardware/smart-sleeve/optical-density.md)
- [OD90 vs OD135](https://khalil-lab.gitbook.io/evolver/hardware/smart-sleeve/optical-density/od90-vs-od135.md)
- [Motherboard Layout and Circuitry](https://khalil-lab.gitbook.io/evolver/hardware/motherboard-layout-and-circuitry.md): This page aims to go more in depth into the Motherboard's circuitry to assist users in making the necessary modifications to add/subtract new experimental parameters or tune existing ones.
- [Arduino](https://khalil-lab.gitbook.io/evolver/hardware/motherboard-layout-and-circuitry/arduino.md): Resources related to using and programming arduinos for eVOLVER.
- [Sensor/Actuator Board Slots](https://khalil-lab.gitbook.io/evolver/hardware/motherboard-layout-and-circuitry/sensor-actuator-board-slots.md)
- [Pulse Width Modulation (PWM) Boards](https://khalil-lab.gitbook.io/evolver/hardware/motherboard-layout-and-circuitry/pulse-width-modulation-pwm-boards.md)
- [Analog-to-Digital Converter (ADC) Boards](https://khalil-lab.gitbook.io/evolver/hardware/motherboard-layout-and-circuitry/analog-to-digital-converter-adc-boards.md)
- [RS485 Board](https://khalil-lab.gitbook.io/evolver/hardware/motherboard-layout-and-circuitry/rs485-board.md)
- [Raspberry Pi](https://khalil-lab.gitbook.io/evolver/hardware/raspberry-pi.md): Resources for setting up and interacting with the Raspberry Pi for use in the eVOLVER platform.
- [Chassis](https://khalil-lab.gitbook.io/evolver/hardware/chassis.md)
- [Light Blocker / Splash Guard](https://khalil-lab.gitbook.io/evolver/hardware/light-blocker-splash-guard.md)
- [Known Issues](https://khalil-lab.gitbook.io/evolver/hardware/known-issues.md)
- [Overview of Software Architecture](https://khalil-lab.gitbook.io/evolver/software/overview-of-software-architecture.md): High-level description of software architecture
- [DPU](https://khalil-lab.gitbook.io/evolver/software/dpu.md): Description of how the DPU (Data Processing Unit) code functions.
- [Calibration](https://khalil-lab.gitbook.io/evolver/software/dpu/calibration.md): An overview of what happens in the software during a calibration
- [custom\_script.py](https://khalil-lab.gitbook.io/evolver/software/dpu/custom_script.py.md): Detailed description of the custom\_script.py file.
- [Experiment Data Files](https://khalil-lab.gitbook.io/evolver/software/dpu/experiment-data-files.md)
- [eVOLVER.py](https://khalil-lab.gitbook.io/evolver/software/dpu/evolver.py.md): Detailed description of the eVOLVER.py file.
- [Arduino](https://khalil-lab.gitbook.io/evolver/software/arduino.md)
- [Server (Raspberry Pi)](https://khalil-lab.gitbook.io/evolver/software/server-raspberry-pi.md): Description of how the Raspberry Pi eVOLVER server code functions.
- [Calibration Files](https://khalil-lab.gitbook.io/evolver/software/server-raspberry-pi/calibration-files.md)
- [Configuration Files (conf.yml)](https://khalil-lab.gitbook.io/evolver/software/server-raspberry-pi/configuration-files-conf.yml.md)
- [Known Issues](https://khalil-lab.gitbook.io/evolver/software/known-issues.md)
- [Adding A New Experimental Parameter](https://khalil-lab.gitbook.io/evolver/extensions/adding-a-new-experimental-parameter.md)
- [Power Supply](https://khalil-lab.gitbook.io/evolver/extensions/adding-a-new-experimental-parameter/power-supply.md)
- [Specific Applications](https://khalil-lab.gitbook.io/evolver/extensions/adding-a-new-experimental-parameter/specific-applications.md)
- [Custom Calibration Code](https://khalil-lab.gitbook.io/evolver/extensions/adding-a-new-experimental-parameter/custom-calibration-code.md)
- [Custom Experiments](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments.md)
- [ePACE](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/epace.md)
- [Experiment Setup](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/epace/experiment-setup.md)
- [ATTiny1634 Writing](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/epace/attiny1634-writing.md)
- [LUX Board Troubleshooting](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/epace/lux-board-troubleshooting.md)
- [Morbidostat](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/morbidostat.md)
- [Extractor Column](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/extractor-column.md)
- [Extractor Volume Maintenance](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/extractor-column/extractor-volume-maintenance.md)
- [Experiment Start](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/extractor-column/experiment-start.md): Setting up and starting an experiment with the extractor set up
- [Sterilizing Extractor Fluidics](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/extractor-column/experiment-start/sterilizing-extractor-fluidics.md): How to set up the extractor fluidics utilizing the slow pump systems
- [Setting up your experiment](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/extractor-column/experiment-start/setting-up-your-experiment.md)
- [Using the extractor script](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/extractor-column/experiment-start/using-the-extractor-script.md)
- [Extractor Analysis](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/extractor-column/extractor-analysis.md)
- [Troubleshooting](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/extractor-column/troubleshooting.md): Possible errors you can run into
- [Example protocols](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/extractor-column/example-protocols.md): Sample protocols of experiments ran using the two column extractor
- [Phototroph Growth](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/phototroph-growth.md)
- [Setup Phototroph eVOLVER](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/phototroph-growth/setup-phototroph-evolver.md)
- [Photo-eVOLVER Smart Sleeves](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/phototroph-growth/photo-evolver-smart-sleeves.md)
- [Photo-eVOLVER Smart Sleeve Construction Guide](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/phototroph-growth/photo-evolver-smart-sleeves/photo-evolver-smart-sleeve-construction-guide.md)
- [Light Calibration](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/phototroph-growth/light-calibration.md)
- [Experiment Guide](https://khalil-lab.gitbook.io/evolver/extensions/custom-experiments/phototroph-growth/experiment-guide.md)
- [Custom Fluidics](https://khalil-lab.gitbook.io/evolver/extensions/custom-fluidics.md)
- [Adding a Third Pump Rack](https://khalil-lab.gitbook.io/evolver/extensions/custom-fluidics/adding-a-third-pump-rack.md)
- [Bubblers / In-Vial Aeration](https://khalil-lab.gitbook.io/evolver/extensions/custom-fluidics/bubblers-in-vial-aeration.md)
- [Bubbler Construction Protocol](https://khalil-lab.gitbook.io/evolver/extensions/custom-fluidics/bubblers-in-vial-aeration/bubbler-construction-protocol.md)
- [Bubbler Cleaning / Testing Apparatus](https://khalil-lab.gitbook.io/evolver/extensions/custom-fluidics/bubblers-in-vial-aeration/bubbler-cleaning-testing-apparatus.md)
- [Bubbler Cleaning Protocol](https://khalil-lab.gitbook.io/evolver/extensions/custom-fluidics/bubblers-in-vial-aeration/bubbler-cleaning-protocol.md)
- [Running the slow pumps](https://khalil-lab.gitbook.io/evolver/extensions/custom-fluidics/running-the-slow-pumps.md)
- [min-eVOLVER](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver.md)
- [About](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/about.md)
- [min-eVOLVER Construction](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/min-evolver-construction.md)
- [Parts](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/min-evolver-construction/parts.md)
- [Construction Protocol](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/min-evolver-construction/construction-protocol.md)
- [Fluidics Setup](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/fluidics-setup.md)
- [Software Installation and Startup](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/software-installation-and-startup.md)
- [send\_command.py](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/send_command.py.md)
- [Calibrations](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/calibrations.md)
- [OD Calibration via Growth Curve](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/calibrations/od-calibration-via-growth-curve.md)
- [Starting an Experiment](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/starting-an-experiment.md)
- [Reusing vial assembly between experiments](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/starting-an-experiment/reusing-vial-assembly-between-experiments.md)
- [ePACE with min-eVOLVER](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/epace-with-min-evolver.md)
- [Experiment Setup](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/epace-with-min-evolver/experiment-setup.md)
- [\[v1.1\] ePACE with min-eVOLVER](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/epace-with-min-evolver/v1.1-epace-with-min-evolver.md)
- [Troubleshooting](https://khalil-lab.gitbook.io/evolver/extensions/min-evolver/troubleshooting.md)
- [Interfacing with Other Systems](https://khalil-lab.gitbook.io/evolver/extensions/interfacing-with-other-systems.md)
- [Guidelines for Contribution](https://khalil-lab.gitbook.io/evolver/contributing/guidelines-for-contribution.md)
- [Reporting a Bug / Hardware Failure](https://khalil-lab.gitbook.io/evolver/contributing/reporting-a-bug-hardware-failure.md)
- [Documentation](https://khalil-lab.gitbook.io/evolver/contributing/documentation.md)
- [Making a Forum Post](https://khalil-lab.gitbook.io/evolver/contributing/documentation/making-a-forum-post.md)
- [How to Edit the Wiki](https://khalil-lab.gitbook.io/evolver/contributing/documentation/how-to-edit-the-wiki.md)
- [Software Development](https://khalil-lab.gitbook.io/evolver/contributing/software-development.md)
- [Hardware Development](https://khalil-lab.gitbook.io/evolver/contributing/hardware-development.md)