/culture_shock

Open-source electroporator for genetic transformation and other culturally shocking activities.

Primary LanguageHTML

Table of Contents

This repository documents how to use and make an electroporator.

Cloning this repo gives you documentation on lab technique and using culture shock, plus a project directory for making printed circuits and related parts of an electroporator, a machine for transforming bacterial suspensions in water to become a new GMO. For how to use culture shock, see Using Culture Shock and Steps Leading up to Transformation. For how to make your own, or something new based on Culture Shock hardware, read on below.

The culture shock electroporator needs some care in using to avoid electrocution hazards -- it may not work out to borrow just some of this project and turn it on -- it really needs its insulating housing to be safe.

Now to describe the project directory and how to use it.

You will notice files that end with .lht or .gvp .sch .bom. Those hold the primary data to generate pcb fab files, or to reuse the circuits to make something else with this as a starting point.

The Project Schematic Representation

The schematic representations of the printed circuits that make up culture shock are edited with the gschem program from the free open source software, (FOSS), project called gEDA Schematic files end in .sch, -- for example kvboard.sch.

The Project Physical Design Representation

The .lht files hold layout data edited with the pcb-rnd FOSS program from here:
http://repo.hu/projects/pcb-rnd/ If it's your first time using pcb or pcb-rnd, start from the begining with this tutorial for pcb, which pcb-rnd is derived from:
http://www.delorie.com/pcb/docs/gs/gs.html

To take a quick look at the state of things without needing to learn to edit them, you can look at image files of the schematics and layout with any browser. Look in directory hardware_schematics_layouts for these files: kvboard.lht.png kvboard.sch.png pyflex_f401.sch.png pyflex_f401.lht pyflex_f401_boost.sch.png. To get ability to zoomin and also edit the schematics and layout, install the software as below on a debian testing installation. It can be easy to start using those schematic and pcb editors -- just give these commands:

sudo apt-get update
sudo apt-get install geda
sudo apt-get install pcb-rnd

then run these commands from the project subdirectory hardware_schematics_layouts created by cloning the culture shock repo:

pcb-rnd kvboard.lht
pcb-rnd micropulser.lht
gschem kvboard.sch micropulser.sch

The schematic and netlist and layout tools used are from the gEDA code: http://wiki.evilmadscientist.com/GEDA_Resources#Basics

Running code on the Culture Shock platform(s)

There are two MCU platforms now -- G30TH is phasing out of use, and PYFLEX_F401 is starting up:

When you connect the culture_shock USB cable to your computer, it will now appear as a "USB mass storage" device. Now you can simply copy the Python (.py) files to the "USB mass storage" drive/folder.

The PYFLEX_F401 platform for micropython has the STM32F401CE MCU

  • voltage converter from USB 5V or battery 3.2 volts up to 18VDC
  • voltage converter from USB 5V down to lithium iron phosphate battery charging at 3.2 volts.
  • 2 20 pin flat flex connectors to get to the GPIOs, ADCs, battery and com ports of the MCU
  • a microUSB AB connector for charging
  • a microUSB AB connector for development and data logging data transfer
  • A 2-wire I2C port can be used with OLED and LCD displays.
  • planned mode to precharge ONBOARD_18V and be ready tp fire a shot, then go back to standby after a minute. (not implemented yet)

Project Module Standard

Flat flex cables, (FFCs), can be symmetric, their connectors are symmetric, and so connection signal vs. pin number order can be reversed by ordinary use of cables and connectors. Using symmetric straight through flat flex cables and connectors is the standard for this project because it simplifies early design prototypes by allowing them to lay flat on the bench with component side of all modules up where one can see and probe them. What symmetric and straight through means by example is: starting with a FFC connector with pins 1 thru 20 with a dot near pin 1 signals connect to another board by going through pin 1 on the first board, straight across without cables being folded or flipped over and into pin 20 of the other board. Pin 2 of the FFC connector on the first board leads to pin 19 on the 2nd, etc.

Using Culture Shock and Steps Leading up to Transformation

Prepare growth media, purify plasmid DNA from a bacterial culture -- Lab Manual.md, then transform E.Coli by electroporation -- Using Culture Shock.

Aiding Development and Debugging

See Developer's Manual to get started with the culture shock and micropython GIT repositories on github, and hook up to culture shock so you can give it commands.

Miscellany

The repo's .gitignore file is set to skip git tracking of .jpg (photos) and .pdf (datasheets) and zipped file bundles, so any of them to distribute need to be saved outside the git repo as a zip file.

Seeing a preview of markdown files like this README.md helps speed documenation. This previewer is useful: grip markdown viewer Grip can serve more than one file at a time with this syntax: grip README.md 6150 grip LAB_MANUAL.md 6151. Doing that helps edit files like this one, (with many links to other files).