Map of Shriram Center for Bioengineering & Chemical Engineering

Biology Team

2017-09-30T21:42:09Z

Chao16:

How to Join SSI Biology

2017-09-30T21:42:04Z

Chao16: Redirected page to Biology Team

#REDIRECT [[Biology Team]]

Wet Lab Access

2017-09-30T21:41:18Z

Chao16:

[[Category:Biology]]

SSI Bio's wetlab access procedures! Please complete all required trainings and submit confirmation to the internal SSI website before your first time in lab.

==SSI Membership==
In order to get clearance for the Uytengsu Teaching Lab (Shriram 114), you need to have SSI membership and do the usual process as well. Check out: [[How to Join SSI]]. Once you've joined SSI, read on!

==Biology STARS Training on Axess==
In addition to your STARS trainings for SSI General Membership, you will also need to complete:

'''EHS-1500 Biosafety'''

Submit a PDF or screenshot of your STARS training confirmation email to the [http://internal.stanfordssi.org/trainings internal site], making sure that your name can be seen in the screenshot.

==Lab Safety Forms & Orientation==
Complete the [https://docs.google.com/a/stanford.edu/forms/d/e/1FAIpQLSehJxmqGn3wmm1_RkTyP04BZEdCrboMDaT2QtXSQw48lM8fOg/viewform?c=0&w=1 Lab Safety Form], read the [https://uytengsuteachinglab.stanford.edu/uytengsu-teaching-lab-policy#Student%20Club Wet Lab Policy], and complete a Lab Safety Orientation - discussed on SSI's Slack (or contact Bio Team Co-Leads). Once confirmed on our side, you should be cleared for access.

==Sign-in Policy==
The Uytengsu Teaching Lab operates on a buddy system, so make sure you have at least one other person with you at all times in lab. Every time you enter the lab, be sure to sign in on the [https://docs.google.com/forms/d/e/1FAIpQLSfejDOAbCvokh5BE3g38dZtpTzeMRDg0lL8AzqgAB0Re8nb8A/viewform?c=0&w=1 UTL sign-in form] and check in with the [https://docs.google.com/document/d/1VVwN54UawYcZKRtW4f62dEiJroYxLaSgLtVFo5u6Axk/edit lifeguard] (usually a BioE or ChemE grad student) on duty. SSI students have permission to work in the Uytengsu Teaching Lab without a lifeguard present as long as there is a safety officer (usually a Bio team co-lead) with you. Current SSI safety officers are Alan Tomusiak and Cynthia Hao, and SSI experiments are typically Thursdays from 7:30-10:00. You must still sign in if there is no lifeguard. Lab coats must be worn at all times in lab. Please leave your food and drink outside on the carts, and put your personal belongings in the lab cubbies for the duration of your work.

After your lab work is done, please clean up all materials you used, put reagents back in the proper places, and sign out of lab using the [https://docs.google.com/forms/d/e/1FAIpQLSdmL5p4lJdvpUU7utMJtBNLSgnnTa0LcMqg0Ezgz80h-29wCg/viewform?c=0&w=1 UTL sign-out form] before leaving.

==Becoming a Safety Officer==
Undergraduate SSI members are eligible to become safety officers once they have taken at least one class in the Uytengsu Teaching Lab space, been given a safety orientation by the lab manager Mong Saetern, and gotten a form filled out and signed by our advisor [[Drew Endy]]. Courses offered include BIOE 44 in autumn and spring quarters, and BIOE 80 in spring. Safety officers will receive key card access to Shriram and the Uytengsu Teaching Lab from 7:00 am to 10:00 pm, and are responsible for the safety of other SSI members working in the lab. At least one safety officer must be present at all times when SSI members are working in the lab.

Wet Lab Access

2017-09-30T21:29:27Z

Chao16:

[[Category:Biology]]

SSI Bio's wetlab access procedures! Please complete all required trainings and submit confirmation to the internal SSI website before your first time in lab.

==SSI Membership==
In order to get clearance for the Uytengsu Teaching Lab (Shriram 114), you need to have SSI membership and do the usual process as well. Check out: [[How to Join SSI]]. Once you've joined SSI, read on!

==Biology STARS Training on Axess==
In addition to your STARS trainings for SSI General Membership, you will also need to complete:

'''EHS-1500 Biosafety'''

Submit a PDF or screenshot of your STARS training confirmation email to the [http://internal.stanfordssi.org/trainings internal site], making sure that your name can be seen in the screenshot.

==Lab Safety Forms & Orientation==
Complete the [https://docs.google.com/a/stanford.edu/forms/d/e/1FAIpQLSehJxmqGn3wmm1_RkTyP04BZEdCrboMDaT2QtXSQw48lM8fOg/viewform?c=0&w=1 Lab Safety Form], read the [https://uytengsuteachinglab.stanford.edu/uytengsu-teaching-lab-policy#Student%20Club Wet Lab Policy], and complete a Lab Safety Orientation - discussed on SSI's Slack (or contact Bio Team Co-Leads). Once confirmed on our side, you should be cleared for access.

==Sign-in Policy==
UTL operates on a buddy system, so make sure you have at least one other person with you at all times in lab. Every time you enter the lab, be sure to sign in on the [https://docs.google.com/forms/d/e/1FAIpQLSfejDOAbCvokh5BE3g38dZtpTzeMRDg0lL8AzqgAB0Re8nb8A/viewform?c=0&w=1 UTL sign-in form] and check in with the [https://docs.google.com/document/d/1VVwN54UawYcZKRtW4f62dEiJroYxLaSgLtVFo5u6Axk/edit lifeguard] (usually a BioE or ChemE grad student) on duty. SSI students have permission to work in the Uytengsu Teaching Lab without a lifeguard present as long as there is a safety officer (usually a Bio team co-lead) with you. Current SSI safety officers are Alan Tomusiak and Cynthia Hao. You must still sign in if there is no lifeguard. Lab coats must be worn at all times in lab. Please leave your food and drink outside on the carts, and put your personal belongings in the lab cubbies for the duration of your work.

After your lab work is done, please clean up all materials you used, put reagents back in the proper places, and sign out of lab using the [https://docs.google.com/forms/d/e/1FAIpQLSdmL5p4lJdvpUU7utMJtBNLSgnnTa0LcMqg0Ezgz80h-29wCg/viewform?c=0&w=1 UTL sign-out form] before leaving.

==Becoming a Safety Officer==
Undergraduate SSI members are eligible to become safety officers once they have taken at least one class in the Uytengsu Teaching Lab space, been given a safety orientation by the lab manager Mong Saetern, and gotten a form filled out and signed by our advisor [[Drew Endy]]. Courses offered include BIOE 44 in autumn and spring quarters, and BIOE 80 in spring. Safety officers will receive key card access to Shriram and the Uytengsu Teaching Lab from 7:00 am to 10:00 pm, and are responsible for the safety of other SSI members working in the lab. At least one safety officer must be present at all times when SSI members are working in the lab.

Slack Directory

2017-09-26T09:08:55Z

Chao16:

== Non-team specific Channels ==
While SSI consists of 6 distinct teams, a large number of channels are general to all SSI members. These channels are great for cross-ssi discussions.
=== General Channels ===
:* #general - typically for general SSI-wide announcements
:* #random - for things you want to share with SSI that doesn’t belong in any other channels
:* #dankmemes - pretty self explanatory. Try typing "/dank" in the channel.
:* #spacenews - to talk about the current state of space affairs
:* #ssipac - politics
:* #best-of-slack - compilation of the best moments on SSI slack
:* #welcome-to-ssi - channel to welcome new members and answer any questions
:* #diverssity - A place to speak about relavant issues
:* #women - A place for women and gender minorities to speak about relavant issues and bond and stuff
:* #new-frosh - for the new frosh to speak among each other about young people problems
=== Fun channels ===
:* #ssi-finds-a-path - DnD roleplaying
:* #ssi-does-exercise - ssi attempts to stay fit
:* #ssi-makes-stuff - a channel to discuss non ssi related personal projects
:* #ssiplacesblocks - ssi’s minecraft group
=== Non team-specific Engineering Channels ===
Interteam collaboration on a technical projects. Why is it called raccoonworks? Who knows.
:* #raccoonworks-eecs - to talk about and get help with random EE or CS related things
:* #raccoonworks-me - to talk about and get help with random ME related things
:* #prak-ssi
=== Class Channels ===
Want to collaborate on a classes with other SSI members? We make channels for classes in the format: #ssitakes[course#]. Ex:
:* #ssitakesme203
:* #ssitakescs106b

== Team Channels ==
Each team has a general announcements channel of the format: #[teamname] (ex #rockets) where general team wide discussion and announcements will be made. Sub-projects, and often subsystems of subprojects will be in their own channels. This is usually where the engineering takes place!
=== Rockets ===
:* #rockets

=== Balloons ===
:* #balloons
:* #balloons-valbal
:* #balloons-rf
:* #balloons-habees
:* #balloons-habhive
:* #habmc
=== Sats ===
:* #satellites
=== Bio ===
:* #biology
:* #biology-reading
:* #biology-terminator
:* #biology-backspace
:* #biology-device
=== Operations ===
:* #operations
:* #operations-herbs
:* #operations-community
:* #operations-diverssity
:* #operations-marketing
=== Policy ===
:* #policy

Contacts
:* {{slack-user|kai}} - operations lead. Talk to him if you want to help make SSI run!
:* {{slack-user|dragland}} and {{slack-user|paigebrown}} - balloons coleads
:* {{slack-user|chao16}} and {{slack-user|tomusiak}} - Biology Co-Leads
:* {{slack-user|johndean}} and {{slack-user|smaldonado}} - Co-Presidents

Biology Team

2017-09-25T20:13:58Z

Chao16:

Find a Project

2017-09-25T06:37:14Z

Chao16:

= SSI Overload =
So you've joined [https://ssi-teams.slack.com/join] Slack, maybe gone to a meeting or two, but you're not sure what you can do or what there even is to do with so many teams swirling around? Well you've come to right place! Below are all the projects each team is working on, what skills they utilize or where they're especially looking for help, and who you can contact to jump in! Think of this like a jobs listing page except that the jobs are always available and you apply by poking the person of contact and saying you want the job -- and it's probably yours.

As you can see from the length of this list, there will always be more SSI to do than you will have hours in a day, week, month, or year -- don't feel pressured to overextend yourself! If you have questions, are feeling overwhelmed, or just want to chat with someone, don't hesitate to reach out to a leadership member. ''SSI exists for, and because of, its members (that's you.) Your sanity, health, and overall well-being always come first.''

= Balloons =

== HABMC ==
HABMC has a request list a mile long, but here are a couple highlights. Feel free to slack {{slack-user|kai}} if you have ideas or questions
* 3D visualizations using Cesium or Unity
* Natural Language Processing for the commands module
* Create a mobile app using React Native
* Improved [[Balloons Radio Projects|RF integrations]]
* Overhaul security on websocket connections
* Navigation algorithms

== ValBal ==

== HABEES ==
HABEES (High Altitude Balloon Electrical Engineering Systems) is the the umbrella project for all EE & CS projects outside of ValBal (that is, largely oriented at standard profile balloon launches). Because of this, there is a nearly limitless number of possibilities and projects to pursue within HABEES -- with that said, if you're new to EE or CS, or a veteran, and just generally want some ideas of what you can make, here's a bunch! Contact {{slack-user|kirillsafin}} to discuss working on any of these!

* HONEY EE -- the primary electronics in HABEES revolve around the HONEY architecture. If you're interested in EE, you can test circuits and/or make PCB's for this architecture and have it fly with other boards. Head over to the [[Gen_2_Architecture | HONEY]] page to understand more about it. Below are some project ideas for circuits/boards you can make for HONEY!
** Motor/Servo Driver
** External/Internal Payload Heaters
** Atmospheric Gas Sensors
** Wind Sensors
** SSTV Radio Board
** WinLink Radio Email Board
** APRS Radio Board
** 12V Battery Management System
** General Purpose Radio Transceiver
** Camera Board
** CubeSat Mapping Board
** Literally anything else
* HONEY CS -- although there's a lot of electronics in HABEES, they all need some software; and, even better, that software always has room for improvement, so here's some possible projects!
** Software for tracking something (with motors/servos)
** Improving filtering/error checking for sensors
** Compression algorithms for logged & transmitted data
** Enhancing speed, quality, and throughput of CAN Bus
** Enhancing TestBench (QueenBee) test software
** Introducing/Developing radio encoding & decoding schemes
** Developing forward & reverse error correction for radio links
** Developing Point-To-Point radar link software

== BUZZ ==
BUZZ is the umbrella subteam for balloons radio projects. It operated as part of HABEES, and works to develop/try/test new radio technologies within balloons. ValBal also develops independent and system-specific radio systems. Some ideas for possible projects, as well as ongoing projects, are below: Talk to {{slack-user|kirillsafin}} and {{slack-user|ariatedjarati}} about them!
* Improved ATV link quality
* Teensy-native SSTV Transmission & Reception
* APRS development
* Native GFSK/FSK/OOK transceivers & software
* WiFi downlink/uplink (2.4GHz / 5 GHz)
* Stanford Ground Station (high gain, directional)
* Portable Field Ground Station
* Balloons National Ground Station Networ
* WinLink Global Radio E-Mail
* Digital Video/Image encoding

= Rockets =
== Onboarding ==

== Daedalus ==

Daedalus is our suite of technology development projects. The work done here pushes forwards on our long-term plan for a space shot. Each project will involve some mechanical, electrical, programming and simulations work, so feel free to join any one of them - but each focuses on a different aspect of rocketry.

Icarus - Reefed Parachute, '''Lead: Saylor'''

*Icarus is building a rocket with a reefed parachute - one which changes size during flight to adjust the rocket descent. This project will intimately involve:
** Mechanics and mechanical engineering - designing, simulating and building a deployment mechanism.
** Mechanics and aerodynamics - designing the parachute and its aerodynamic properties.
** Electrical engineering - PCB design, electrical integration and programming. Focus on high reliability and low size & power.

Charybdis - Spin Stabilization '''Contact: William'''

*Charybdis is building a rocket that spins like a rifle bullet, then stops spinning mid-air to deploy parachutes.
** Mechanical engineering - designing reliable deployment mechanism.
** Aerodynamics and simulation - designing fin system to create desired spin.

Argus - Distributed RF Camera System '''Lead: John'''

*Argus is building a rocket equipped with a new camera system, allowing us to easily take video (and possibly stream live!) from the interior and exterior of rockets as they fly.
** Electrical Engineering - circuit board design, electrical integration.
** Signals - RF & transmission tech.

== Competition (IREC/SA Cup) ==
* Structures
* Payload
* Recovery
* Avionics, '''Leads: Sharon, Julea''' {{slack-user|splatt}} {{slack-user|juleachin}}
** Design, implement, and test all the hardware and software that goes into our flight computers
** Design and manufacture structures for avionics bay and work with other subteams to implement interfaces and integration processes
** Design and test radio communications system for our rocket to talk to the ground
** Write software to parse and visualize data, build a protective cooling case for laptops & other electronics so they don't die in the blazing desert heat and dust (yes there's a story here)
* Launch Operations, '''Lead: WANTED'''
** Work with each subteam to coordinate and prepare launch materials
** Plan & execute travel and launch logistics
** Oversee launch procedures, checklists, and go/no calls
** Many more additional projects for ground support designable around personal interests
* Simulations

= Satellites =
=== STAR-CROSSED===
The Stanford Timing And Ranging –Cross-linking Optical Small Satellite Demonstration mission is an ambitious proposal seeking to place two cubesats in low Earth orbit and establish a laser-based data link between them across hundreds of kilometers. Such a mission has never before been attempted. If successful, the technology developed will enable a dramatic leap forward in the capabilities of both cubesats and larger satellitesto communicate high volumes of data across long distances.

Optical links using lasers are capable of dramatically higher data transmission speeds than existing radio systems, but have never been successfully demonstrated at the cubesat scale. A cubesat-sized optical communications system willenable high-speed links between cubesats, allowing for networks built from affordable satellites.Miniaturizing an optical communications system to fit in a cubesat would also make it far easier for larger satellites to add optical networking capabilities, an almost essential component of proposed internet satellite constellations.

Satellites with optical links can not only transmit data faster, but also better synchronize their timekeeping with each other and measure their separation distance, important features of boththe GPS system and groups of scientific satellites. With an optical network, satellites could conduct previously impossible scientific missions and significantly improve the accuracy of GPS

Now is the perfect time to get involved with STAR-CROSSD. A number of subsystems need to be analyzed, designed, built, and tested, with opportunities to learn about electrical, mechanical, and software engineering, satellite operations, and more.

=== POINTR ===
Polar Orbiting INfrared Tracking Receiver (POINTR) has been Satellites’ primary focus since February. POINTR is an in flight demonstration of an optical receiver pointing, acquisition and tracking (PAT) system. The optical receiver payload hosted on Audacy’s 3U cubesat would be pointed to the ground to acquire and track a beacon laser sent from a suitable ground facility, currently proposed as NASA JPL’s OCTL facility. This mission would demonstrate the operational and technical requirements related to two satellites establishing an optical communications link with each other. The requirements include mission planning, command and execution of a pointing maneuver, acquisition of an incoming optical signal and tracking of the optical signal. This mission can be broken into four main goals:

* Demonstrate a subset of technology for full bidirectional optical communications mission within the constraints placed by Audacy’s primary mission.

* Increase chance of bidirectional optical communications mission success.

* Develop experience within SSI designing and building space hardware.

* Contribute to the cubesat and satellite optical communications technical fields.

=== Our Subteams ===
* '''Avionics'''
**'''The Gist'''The Avionics group works on all of the core electrical systems for the Satellites team, including electrical power distribution, sensors, and computing. Learn how to design and reflow Printed Circuit Boards (PCBs) and work with signal-processing to understand light signals in the inky darkness of space!
**'''The People To Talk to''' Sasha, Shi, Meera

* '''GNC'''
**'''The Gist''' The GNC group ("Guidance, Navigation, and Control") is responsible for determining and controlling the position and rotation of satellites in space even while hundreds or sometimes thousands of miles away. Join GNC to work with us on cutting-edge technologies and a system to control our satellites in orbit from the comfort of the SSI space bunker.
**'''The People To Talk to''' Sasha

* '''Optics'''
**'''The Gist''' Optics is all about putting light to work - starting from simple laser pointers to finally sending a communications signal across 10 kilometers in space! We use lasers, lenses, filters, sensors and even moving mirrors to send light flying through space and catch it on the other side.
**'''The People To Talk to''' Michael Taylor

* '''Software'''
**'''The Gist''' The software team tackles the many different challenges of software needed for satellites: from flight software to web development, we do it all. For flight software, we take advantage of parallel communications modules to manage real-time requirements on pointing control. For web development, we are partnering with the ground operations team to build thorough mission control software and web interface. If any of this seems daunting or complicated, don’t worry. We all started from scratch. Join software and get your code in space!
**'''The People To Talk to''' Orien, Joan

* '''Ground Ops'''
**'''The Gist''' The Ground Operations team will build mission control software and web interface to analyze satellite behavior in-flight and react accordingly. Aside from software, physics and orbital mechanics are crucial parts of this team’s ability. This team is responsible for testing spacecraft stability, fault tolerance, and final mission success.
**'''The People To Talk to''' Orien

*'''Structures'''
**'''The Gist''' The Structures team designs and builds all necessary flight mechanics, ranging from the overall structure to individual component mounts. We go through the full development process - whiteboard drawings, SolidWorks, and finally manufacturing.The Structures team is also responsible for many of the environmental considerations, such as the thermal and vacuum requirements of space, as well as the shock and vibration profile of launch.
**'''The People To Talk to''' Anjali, Sandip

= Biology =

* Enzymatic DNA Synthesis Methods, '''Lead: Michael Uttmark''' {{slack-user|uttmark}}
** Test commercial blocking groups for compatibility with [[Terminal Deoxynucleotidyl Transferase]]
** Chemically synthesize nucleotides with different reversible blocking groups
** Characterize and optimize [[Enzymatic Synthesis Methods | enzymatic DNA synthesis]] reaction efficiency
** Build and run stochastic computer models of DNA synthesis to optimize reaction parameters
** Research purification methods for synthesized DNA
** Design and test your own synthesis method!
* Sequence Verification
** Execute and optimize any one of our existing verification procedures--[[Polyacrylamide Gel Electrophoresis]], [[Pyrosequencing]], or [[Ligation and Sequencing]]
** Adapt LCMS or MALDI-TOF procedures for detecting single-base addition or determining the sequence of a sample.
** Come up with new ways to verify single-base addition to a starting strand of DNA
* Microfluidic Device Design
** Design and program an [[Electrowetting on Dielectric]] microfluidic PCB
** Simulate and test how a microfluidic system would work in microgravity
** Port our DNA synthesis method to a solid substrate like controlled pore glass or streptavidin-biotin magnetic beads
** Optimize an integrated microfluidic protocol for DNA synthesis and verification on the electrowetting PCB and on the [[Beckman Biomek 2000]] liquid handling robot in lab
** Research and test other automated [https://en.wikipedia.org/wiki/Microfluidics fluid handling methods], like [https://en.wikipedia.org/wiki/Acoustic_droplet_ejection acoustic droplet ejection] or [https://en.wikipedia.org/wiki/Optoelectrowetting optoelectrowetting].
** Build a system for cooling and temperature control of the device, perhaps using [https://en.wikipedia.org/wiki/Thermoelectric_cooling Peltiers]
** Write an algorithm to minimize the number of groups of compatible templates needed for the [[Enzymatic Synthesis Methods | exonuclease method]]
** Figure out how to power our PCB from a cubesat or other launch vehicle
** Build testing rigs for DNA synthesis methods that are needed for experiments in lab

= Policy =

= Operations =

== Community ==
* Come up with a theme for Special Dinner and make decorations (like a model Falcon 9!)
* Help {{slack-user|dragland}} run SSI general dinners
* Plan and run general community events like Trivia Night, Pathfinder, and Movie Night
== Diversity ==
* Build connections with engineering diversity groups on campus
* Help {{slack-user|ruqayyatoorawa}} run workshops
== Events ==
* Find an interesting company and arrange a tour or talk
* Help handle logistics of an existing talk, like by meeting an astronaut and walking him to Durand 450
* Give a CEO or Venture Capitalist a tour of ESIII
== Finance ==
* Complete reimbursements
* Apply for grants & seek out new sponsors
== Marketing ==
* Design awesome swag (t-shirts, jackets, posters)
* Reach out to reporters
* Social media guru! (Facebook, Twitter, and Instagram posts)
* Creating Snapchat filters for events
* Designing flyers for upcoming talks
* Going on launches to take pictures and videos
== Outreach ==
* Start discussions with local highschools and their science clubs
* Organize or join an existing trip to a local school
== Sponsors ==
* Pursue a sponsorship (we'll walk you through how!)
* Compile a list of bay-area aerospace companies
== Website ==
* Overhaul the budgeting system
* Give the sponsors page dynamic content
* Manage this very wiki
* Manage our public and internal websites
== Workspace ==
* Make space-themed artwork to decorate ESIII
* Plant more herbs
* Paint a mural
* Track inventory of supplies and parts

[[Category:Getting started]]

Find a Project

2017-09-25T06:06:51Z

Chao16:

= SSI Overload =
So you've joined [https://ssi-teams.slack.com/join] Slack, maybe gone to a meeting or two, but you're not sure what you can do or what there even is to do with so many teams swirling around? Well you've come to right place! Below are all the projects each team is working on, what skills they utilize or where they're especially looking for help, and who you can contact to jump in! Think of this like a jobs listing page except that the jobs are always available and you apply by poking the person of contact and saying you want the job -- and it's probably yours.

As you can see from the length of this list, there will always be more SSI to do than you will have hours in a day, week, month, or year -- don't feel pressured to overextend yourself! If you have questions, are feeling overwhelmed, or just want to chat with someone, don't hesitate to reach out to a leadership member. ''SSI exists for, and because of, its members (that's you.) Your sanity, health, and overall well-being always come first.''

= Balloons =

== HABMC ==
HABMC has a request list a mile long, but here are a couple highlights. Feel free to slack {{slack-user|kai}} if you have ideas or questions
* 3D visualizations using Cesium or Unity
* Natural Language Processing for the commands module
* Create a mobile app using React Native
* Improved [[Balloons Radio Projects|RF integrations]]
* Overhaul security on websocket connections
* Navigation algorithms

== ValBal ==

== HABEES ==
HABEES (High Altitude Balloon Electrical Engineering Systems) is the the umbrella project for all EE & CS projects outside of ValBal (that is, largely oriented at standard profile balloon launches). Because of this, there is a nearly limitless number of possibilities and projects to pursue within HABEES -- with that said, if you're new to EE or CS, or a veteran, and just generally want some ideas of what you can make, here's a bunch! Contact {{slack-user|kirillsafin}} to discuss working on any of these!

* HONEY EE -- the primary electronics in HABEES revolve around the HONEY architecture. If you're interested in EE, you can test circuits and/or make PCB's for this architecture and have it fly with other boards. Head over to the [[Gen_2_Architecture | HONEY]] page to understand more about it. Below are some project ideas for circuits/boards you can make for HONEY!
** Motor/Servo Driver
** External/Internal Payload Heaters
** Atmospheric Gas Sensors
** Wind Sensors
** SSTV Radio Board
** WinLink Radio Email Board
** APRS Radio Board
** 12V Battery Management System
** General Purpose Radio Transceiver
** Camera Board
** CubeSat Mapping Board
** Literally anything else
* HONEY CS -- although there's a lot of electronics in HABEES, they all need some software; and, even better, that software always has room for improvement, so here's some possible projects!
** Software for tracking something (with motors/servos)
** Improving filtering/error checking for sensors
** Compression algorithms for logged & transmitted data
** Enhancing speed, quality, and throughput of CAN Bus
** Enhancing TestBench (QueenBee) test software
** Introducing/Developing radio encoding & decoding schemes
** Developing forward & reverse error correction for radio links
** Developing Point-To-Point radar link software

== BUZZ ==
BUZZ is the umbrella subteam for balloons radio projects. It operated as part of HABEES, and works to develop/try/test new radio technologies within balloons. ValBal also develops independent and system-specific radio systems. Some ideas for possible projects, as well as ongoing projects, are below: Talk to {{slack-user|kirillsafin}} and {{slack-user|ariatedjarati}} about them!
* Improved ATV link quality
* Teensy-native SSTV Transmission & Reception
* APRS development
* Native GFSK/FSK/OOK transceivers & software
* WiFi downlink/uplink (2.4GHz / 5 GHz)
* Stanford Ground Station (high gain, directional)
* Portable Field Ground Station
* Balloons National Ground Station Networ
* WinLink Global Radio E-Mail
* Digital Video/Image encoding

= Rockets =
== Onboarding ==

== Daedalus ==

Daedalus is our suite of technology development projects. The work done here pushes forwards on our long-term plan for a space shot. Each project will involve some mechanical, electrical, programming and simulations work, so feel free to join any one of them - but each focuses on a different aspect of rocketry.

Icarus - Reefed Parachute, '''Lead: Saylor'''

*Icarus is building a rocket with a reefed parachute - one which changes size during flight to adjust the rocket descent. This project will intimately involve:
** Mechanics and mechanical engineering - designing, simulating and building a deployment mechanism.
** Mechanics and aerodynamics - designing the parachute and its aerodynamic properties.
** Electrical engineering - PCB design, electrical integration and programming. Focus on high reliability and low size & power.

Charybdis - Spin Stabilization '''Contact: William'''

*Charybdis is building a rocket that spins like a rifle bullet, then stops spinning mid-air to deploy parachutes.
** Mechanical engineering - designing reliable deployment mechanism.
** Aerodynamics and simulation - designing fin system to create desired spin.

Argus - Distributed RF Camera System '''Lead: John'''

*Argus is building a rocket equipped with a new camera system, allowing us to easily take video (and possibly stream live!) from the interior and exterior of rockets as they fly.
** Electrical Engineering - circuit board design, electrical integration.
** Signals - RF & transmission tech.

== Competition (IREC/SA Cup) ==
* Structures
* Payload
* Recovery
* Avionics, '''Leads: Sharon, Julea''' {{slack-user|splatt}} {{slack-user|juleachin}}
** Design, implement, and test all the hardware and software that goes into our flight computers
** Design and manufacture structures for avionics bay and work with other subteams to implement interfaces and integration processes
** Design and test radio communications system for our rocket to talk to the ground
** Write software to parse and visualize data, build a protective cooling case for laptops & other electronics so they don't die in the blazing desert heat and dust (yes there's a story here)
* Launch Operations, '''Lead: WANTED'''
** Work with each subteam to coordinate and prepare launch materials
** Plan & execute travel and launch logistics
** Oversee launch procedures, checklists, and go/no calls
** Many more additional projects for ground support designable around personal interests
* Simulations

= Satellites =
=== STAR-CROSSED===
The Stanford Timing And Ranging –Cross-linking Optical Small Satellite Demonstration mission is an ambitious proposal seeking to place two cubesats in low Earth orbit and establish a laser-based data link between them across hundreds of kilometers. Such a mission has never before been attempted. If successful, the technology developed will enable a dramatic leap forward in the capabilities of both cubesats and larger satellitesto communicate high volumes of data across long distances.

Optical links using lasers are capable of dramatically higher data transmission speeds than existing radio systems, but have never been successfully demonstrated at the cubesat scale. A cubesat-sized optical communications system willenable high-speed links between cubesats, allowing for networks built from affordable satellites.Miniaturizing an optical communications system to fit in a cubesat would also make it far easier for larger satellites to add optical networking capabilities, an almost essential component of proposed internet satellite constellations.

Satellites with optical links can not only transmit data faster, but also better synchronize their timekeeping with each other and measure their separation distance, important features of boththe GPS system and groups of scientific satellites. With an optical network, satellites could conduct previously impossible scientific missions and significantly improve the accuracy of GPS

Now is the perfect time to get involved with STAR-CROSSD. A number of subsystems need to be analyzed, designed, built, and tested, with opportunities to learn about electrical, mechanical, and software engineering, satellite operations, and more.

=== POINTR ===
Polar Orbiting INfrared Tracking Receiver (POINTR) has been Satellites’ primary focus since February. POINTR is an in flight demonstration of an optical receiver pointing, acquisition and tracking (PAT) system. The optical receiver payload hosted on Audacy’s 3U cubesat would be pointed to the ground to acquire and track a beacon laser sent from a suitable ground facility, currently proposed as NASA JPL’s OCTL facility. This mission would demonstrate the operational and technical requirements related to two satellites establishing an optical communications link with each other. The requirements include mission planning, command and execution of a pointing maneuver, acquisition of an incoming optical signal and tracking of the optical signal. This mission can be broken into four main goals:

* Demonstrate a subset of technology for full bidirectional optical communications mission within the constraints placed by Audacy’s primary mission.

* Increase chance of bidirectional optical communications mission success.

* Develop experience within SSI designing and building space hardware.

* Contribute to the cubesat and satellite optical communications technical fields.

=== Our Subteams ===
* '''Avoinics'''
**'''The Jist'''The Avionics group works on all of the core electrical systems for the Satellites team, including electrical power distribution, sensors, and computing. Learn how to design and reflow Printed Circuit Boards (PCBs) and work with signal-processing to understand light signals in the inky darkness of space!
**'''The People To Talk to''' Sasha, Shi, Meera

* '''GNC'''
**'''The Jist''' The GNC group ("Guidance, Navigation, and Control") is responsible for determining and controlling the position and rotation of satellites in space even while hundreds or sometimes thousands of miles away. Join GNC to work with us on cutting-edge technologies and a system to control our satellites in orbit from the comfort of the SSI space bunker.
**'''The People To Talk to''' Sasha

* '''Optics'''
**'''The Jist''' Optics is all about putting light to work - starting from simple laser pointers to finally sending a communications signal across 10 kilometers in space! We use lasers, lenses, filters, sensors and even moving mirrors to send light flying through space and catch it on the other side.
**'''The People To Talk to''' Michael Taylor

* '''Software'''
**'''The Jist''' The software team tackles the many different challenges of software needed for satellites: from flight software to web development, we do it all. For flight software, we take advantage of parallel communications modules to manage real-time requirements on pointing control. For web development, we are partnering with the ground operations team to build thorough mission control software and web interface. If any of this seems daunting or complicated, don’t worry. We all started from scratch. Join software and get your code in space!
**'''The People To Talk to''' Orien, Joan

* '''Ground Ops'''
**'''The Jist''' The Ground Operations team will build mission control software and web interface to analyze satellite behavior in-flight and react accordingly. Aside from software, physics and orbital mechanics are crucial parts of this team’s ability. This team is responsible for testing spacecraft stability, fault tolerance, and final mission success.
**'''The People To Talk to''' Orien

*'''Structures'''
**'''The Jist''' The Structures team designs and builds all necessary flight mechanics, ranging from the overall structure to individual component mounts. We go through the full development process - whiteboard drawings, SolidWorks, and finally manufacturing.The Structures team is also responsible for many of the environmental considerations, such as the thermal and vacuum requirements of space, as well as the shock and vibration profile of launch.
**'''The People To Talk to''' Anjali, Sandip

= Biology =

* Enzymatic DNA Synthesis Methods with Blocking Groups, '''Lead: Michael Uttmark''' {{slack-user|uttmark}}
** Test commercial blocking groups for compatibility with [[Terminal Deoxynucleotidyl Transferase]]
** Chemically synthesize nucleotides with different reversible blocking groups
** Characterize and optimize [[Enzymatic Synthesis Methods | enzymatic DNA synthesis]] reaction efficiency
** Model DNA synthesis stochastically to optimize reaction parameters.
** Research purification methods for synthesized DNA
** Design and test your own synthesis method!
* Sequence Verification
** Execute and optimize any one of our existing verification procedures--[[Polyacrylamide Gel Electrophoresis]], [[Pyrosequencing]], or [[Ligation and Sequencing]]
** Adapt LCMS or MALDI-TOF procedures for detecting single-base addition or determining the sequence of a sample.
** Come up with new ways to verify single-base addition to a starting strand of DNA
* Microfluidic Device Design
** Design and program an [[Electrowetting on Dielectric]] microfluidic PCB
** Simulate and test how a microfluidic system would work in microgravity
** Port our DNA synthesis method to a solid substrate like controlled pore glass or streptavidin-biotin magnetic beads
** Optimize an integrated microfluidic protocol for DNA synthesis and verification on the electrowetting PCB and on the [[Beckman Biomek 2000]] liquid handling robot in lab
** Research and test other automated [https://en.wikipedia.org/wiki/Microfluidics fluid handling methods], like [https://en.wikipedia.org/wiki/Acoustic_droplet_ejection acoustic droplet ejection] or [https://en.wikipedia.org/wiki/Optoelectrowetting optoelectrowetting].
** Build a system for cooling and temperature control of the device, perhaps using [https://en.wikipedia.org/wiki/Thermoelectric_cooling Peltiers]
** Figure out how to power our PCB from a cubesat or other launch vehicle
** Build testing rigs for DNA synthesis methods that are needed for experiments in lab

= Policy =

= Operations =

== Community ==
* Come up with a theme for Special Dinner and make decorations (like a model Falcon 9!)
* Help {{slack-user|dragland}} run SSI general dinners
* Plan and run general community events like Trivia Night, Pathfinder, and Movie Night
== Diversity ==
* Build connections with engineering diversity groups on campus
* Help {{slack-user|ruqayyatoorawa}} run workshops
== Events ==
* Find an interesting company and arrange a tour or talk
* Help handle logistics of an existing talk, like by meeting an astronaut and walking him to Durand 450
* Give a CEO or Venture Capitalist a tour of ESIII
== Finance ==
* Complete reimbursements
* Apply for grants & seek out new sponsors
== Marketing ==
* Design awesome swag (t-shirts, jackets, posters)
* Reach out to reporters
* Social media guru! (Facebook, Twitter, and Instagram posts)
* Creating Snapchat filters for events
* Designing flyers for upcoming talks
* Going on launches to take pictures and videos
== Outreach ==
* Start discussions with local highschools and their science clubs
* Organize or join an existing trip to a local school
== Sponsors ==
* Pursue a sponsorship (we'll walk you through how!)
* Compile a list of bay-area aerospace companies
== Website ==
* Overhaul the budgeting system
* Give the sponsors page dynamic content
* Manage this very wiki
* Manage our public and internal websites
== Workspace ==
* Make space-themed artwork to decorate ESIII
* Plant more herbs
* Paint a mural
* Track inventory of supplies and parts

[[Category:Getting started]]

2017-09-14T05:48:33Z

Chao16: Redirected page to Enzymatic Synthesis Methods

#REDIRECT [[Enzymatic Synthesis Methods]]

Pyrosequencing

2017-09-14T05:45:48Z

Chao16: Created page with "Pyrosequencing is a sequencing technique that uses a four-enzyme pathway to detect the addition of nucleotides to a strand of DNA. Pyrosequencing is compatible with Electrow..."

Pyrosequencing is a sequencing technique that uses a four-enzyme pathway to detect the addition of nucleotides to a strand of DNA. Pyrosequencing is compatible with [[Electrowetting on Dielectric]] microfluidics systems.

==Overview==
[[File:Pyrosequencing_diagram.png|thumb|right| Pyrosequencing enzyme pathway]]
In commercial pyrosequencing, the strand to be sequenced is immobilized on magnetic beads and used as a template for a template-dependent polymerase. One type of nucleotide at a time is introduced to the DNA with enzyme mix to build up the complementary sequence to this strand.

1. When the correct type of nucleotide is added onto the complementary DNA strand by a template-dependent polymerase, pyrophosphate (PPi) is released as a byproduct of the DNA backbone formation reaction.

2. The reaction of this pyrophosphate and adenosine phosphosulfate (APS) to form ATP is then catalyzed by ATP sulfurylase.

3. The ATP produced then powers the conversion of luciferin substrate into a luminescence signal almost instantaneously by firefly luciferase. The light signal resulting from each nucleotide addition lasts about 10 minutes and can be measured by a photomultiplier tube.

4. Pyrosequencing can be sped up with the addition of apyrase, which degrades luminescence signal quickly and allows for the next nucleotide to be added. Alternatively, unreacted reagents and nucleotides can be washed off the DNA before the introduction of the next nucleotide type.

If luminescence is detected, the type of nucleotide that was added is recorded, and the process of adding nucleotides is continued until the full sequence of the complementary strand is known.

To control the reaction steps, pyrosequencing reagents are typically separated into enzyme mix (containing ATP sulfurylase, polymerase, luciferin, and luciferase) and substrate mix (containing APS and one type of nucleotide). The nucleotide 2'-Deoxyadenosine-5'-O-(1-Thiotriphosphate), or dATPαS, is used in place of dATP in pyrosequencing reactions since dATP is a substrate for luciferase and will give a false positive luminescence signal.
Luminescence signal is linearly proportional to the number of nucleotides added (up to about 4 or 5 bases), so a sequence of two or more of the same type of nucleotide in a row (a homopolymer) can be distinguished from addition of a single base.

The [https://www.qiagen.com/us/shop/automated-solutions/sequencers/pyromark-q24/#resources Qiagen Pyromark] system and the [Roche 454 Sequencing]

==Modified Pyrosequencing==
SSI Biology uses a modified version of pyrosequencing to quickly detect extension of a starting single strand of DNA instead of the sequence of a strand. [[Terminal Deoxynucleotidyl Transferase | TdT]] or another of our [[Enzymatic Synthesis Methods]] is used to add a known base instead of polymerase. The pyrophosphate from this addition can then be converted to a luminescence signal and detected. Luminescence indicates successful addition of one or more bases to the DNA. By comparing signal level to signal produced by a control addition reaction with blocked bases, we can also determine whether an insertion error occurred (more than one base was added).

==Sample Procedure==
A starting oligonucleotide of DNA is extended with a desired nucleotide and one of the [[Enzymatic Synthesis Methods]] listed above. The solution containing pyrophosphates (this can be the unpurified extended DNA sample or the waste after the DNA is purified) is combined with 3x enzyme mix (13.5 mU/uL ATP Sulfurylase, 1.5 ug/uL luciferase, and 1.8 ug/uL luciferin in pyrosequencing buffer) and 3.09x substrate mix (7.5 ug/uL APS in pyrosequencing buffer) in the correct dilution for a total sample volume of 20 uL. A reducing agent such as dithiothreitol or TCEP can be added but is not necessary for the reaction to occur. The samples should be mixed thoroughly and measured as soon after adding enzyme mix as possible. Samples are transferred to a 96-well plate for measurement and loaded into a plate reader, which will read out luminescence values for the sample over a given time period.

An example protocol for a basic pyrosequencing experiment can be found [https://www.overleaf.com/10631311fvwdhpzhfxjx#/39800360/ here].

==References==
Boles, Deborah J., et al. "Droplet-based pyrosequencing using digital microfluidics." Analytical chemistry 83.22 (2011): 8439-8447. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690483/]

[[Category: Biology]]

File:Pyrosequencing diagram.png

2017-09-14T05:26:17Z

Chao16: Pyrosequencing enzyme diagram

Pyrosequencing enzyme diagram

Ligation and Sequencing

2017-09-13T08:03:52Z

Chao16: Created page with "==Overview== Ligation and Sequencing is a method to detect single or multiple base addition to a single strand of DNA by Enzymatic Synthesis Methods. This detection method..."

==Overview==
Ligation and Sequencing is a method to detect single or multiple base addition to a single strand of DNA by [[Enzymatic Synthesis Methods]]. This detection method involves sequencing the added bases with a commercial sequencing service. The segment to be sequenced is effectively put in the middle of the starting DNA to avoid poor quality sequencing reads usually encountered at the ends of linear DNA.

==Starting DNA==
Instead of adding to a DNA oligonucleotide (~15 nt long), the addition will be performed on a single linear DNA strand with a known sequence that is long enough to be circularized (~1 kb). Long single-stranded DNA can be obtained by cutting a [https://www.neb.com/products/n4040-m13mp18-single-stranded-dna#pd-description single-stranded DNA plasmid] with restriction enzymes. Single-stranded DNA cannot be amplified by PCR.

==Ligation==
Once multiple bases have been added to the linear single strand of DNA, the DNA will be circularized with [http://www.epibio.com/enzymes/ligases-kinases-phosphatases/dna-ligases/circligase-ssdna-ligase?details single-stranded DNA ligase]. If the DNA is not circularized, the extended 3' end will be ligated to the 5' end of another linear piece of DNA, resulting in the same desired sequence.

==Sequencing==
Once the DNA sample is purified to remove any remaining nucleotides or enzyme, the circularized DNA can be sent for sequencing by a commercial sequencing service. The primer used to sequence the DNA should be a reverse primer taken from ~200 nt downstream of the 5' end of the original linear starting DNA. The sequencing results should reveal which bases were added and give a rough quantification of addition efficiency.

Terminal Deoxynucleotidyl Transferase

2017-09-13T07:28:44Z

Chao16:

[[File:Tdt infocard.jpeg|frame|right|A graphical primer on TdT]]
==Overview==
Terminal Deoxynucleotidyl Transferase (TdT) is a template-independent DNA polymerase, meaning that it can add DNA bases to an existing single strand of DNA without the sequence being dictated by a longer complementary strand. TdT must have a starting strand of DNA 3 base pairs long, and it adds to the 3' end of the strand like most polymerases. TdT can use many different nucleotides as substrates, incorporating a huge variety of natural and synthetic nucleotides, whether [[Blocking Groups|blocked]] or unblocked, although it prefers to add dGTP and dCTP and avoids dATP. It is also suspected that TdT adds completely distributively, detaching from and reattaching to each strand between addition events instead of staying on one strand of DNA. In nature, TdT is used for DNA repair and to generate random antibodies in the immune system. SSI Biology is using recombinant bovine TdT to extend starting strands of DNA with an arbitrary sequence of bases for ''de novo'' DNA synthesis.

==Structure==
TdT is shaped like a right hand like most polymerases, with a metal ion-containing "palm" domain where the extension reaction occurs, "fingers" to align the DNA strand and nucleotide properly, and an "index finger" and "thumb" to guide nucleotides into the enzyme active site. However, TdT contains a 16-amino acid loop that only lets in single stranded DNA for binding, and not double stranded DNA.

==Divalent Cations==
TdT uses divalent cations as catalysts to extend DNA, and the efficiency of the reaction is affected by the type of cation used. Zinc and magnesium cations work best for extension, with magnesium causing TdT to prefer dGTP and dATP. Most commercial TdT buffers (such as the one SSI Biology currently uses) contain cobalt, which leads to preferential addition of dCTP and dTTP. [https://en.wikipedia.org/wiki/Ethylenediaminetetraacetic_acid Ethylenediaminetetraacetic acid (EDTA)] inactivates TdT by chelating all of the divalent cations so that the addition reaction cannot occur.

==Generic TdT Extension Protocol==
TdT is incubated with a starting primer, nucleotides, TdT buffer, and nuclease-free water at 37C for thirty minutes to an hour. Once the reaction is complete, TdT can be heat-inactivated by raising temperature to 70C for 10 minutes. EDTA can also be added to inactivate the enzyme and stop the reaction. TdT should be stored at -20C.

==References==
Motea, Edward A., and Anthony J. Berdis. “Terminal Deoxynucleotidyl Transferase: The Story of a Misguided DNA Polymerase.” Biochimica et biophysica acta 1804.5 (2010): 1151–1166. PMC. Web. 10 Sept. 2017. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846215/]

[[Category:Biology]]

Polyacrylamide Gel Electrophoresis

2017-09-12T06:48:37Z

Chao16:

==Overview==
Polyacrylamide gel electrophoresis (PAGE) is a method of separating DNA fragments by length. DNA fragments are loaded into a gel made of many acrylamide polymers. A voltage differential is applied across the gel, causing the negatively charged DNA fragments to move down the gel. Shorter fragments will encounter less resistance from the gel matrix and travel further than longer fragments in the same amount of time. The gel is later stained with a fluorescent DNA binding dye so that the DNA can be seen as bands in a blue light or UV imager. Typically, a DNA ladder with DNA fragments of known size is loaded into the gel as a "ruler" for samples to be compared against.

The higher the concentration of the gel, the slower all DNA travels through it, enabling a higher resolution to be obtained. Single stranded DNA will travel faster than double stranded DNA. Plasmid (circularized) DNA will travel faster on a gel and appear shorter than linear DNA of the same length.

==Single Nucleotide Addition Detection==
By adding desired nucleotides one base at a time using [[Enzymatic Synthesis Methods]], a completely arbitrary sequence of DNA can be created without an existing template sequence. SSI Biology uses PAGE to detect addition of exactly one nucleotide to an existing strand of single-stranded DNA. We currently use 15% pre-cast gels and SYBR Gold gel stain for imaging the DNA.

==Safety==
Polyacrylamide is a neurotoxin when in liquid form. However, this is only a concern when casting gels from liquid polyacrylamide. We only use pre-cast polyacrylamide gels, which are delivered in solid form and are non-hazardous.

==Procedure==

===Setting up the gel apparatus===
[[File:Gel apparatus.JPG|thumb|right| PAGE gel apparatus and gel box.]]
SSI Biology currently uses the Bio-Rad Mini PROTEAN Tetra Cell apparatus.

Take a 15% TBE-Urea denaturing pre-cast gel out of its package, remove the green tape from the bottom of the gel, and carefully remove the comb from the top of the gel. Slot the gel and a buffer dam into the gel apparatus and push the green wings inwards, making sure there are no gaps where the gel meets the bottom tabs of the apparatus and that the right sides of the gel and the buffer dam are facing outwards. A second gel can be placed into the gel apparatus instead of the buffer dam. Place the gel apparatus into its clear box, making sure that the positive (red) electrode is closer to the red mark on the box. Fill the apparatus with .5x Tris-Borate-EDTA (TBE) running buffer, stopping to seal any leaks. Let the buffer overflow into the gel box up to the level marked on the box. Up to four gels can be run at once in the same box. Pipette TBE buffer up and down into the each well of the gel to rinse out any urea residue. Place the green lid onto the box and pre-run the gel for 20 minutes at your desired voltage.

===Loading samples===
[[File:Loading_dye.jpg|thumb|right| Gels should be stopped when the darker dye front is 1 cm from the bottom.]]
Prepare your DNA samples by mixing them with 2x Gel Loading Buffer II (containing the denaturing agent formamide and bromophenol blue and xylene cyanol dyes). Take the lid off the gel box, and rinse the wells with TBE buffer before loading your samples. Pipette each sample carefully into one well, so as to avoid bubbles or overflow into other wells. Cover the gel box with the green lid and connect the lid to the power supply. Run the gel at 150V until the dark blue dye (the first dye front) gets to about 1 cm from the bottom of the gel.

===Staining the gel===
Turn off the power supply, open the gel box, and disassemble the gel apparatus. Carefully pry the gel apart with a lever or spatula. Slide the gel from the plastic cover into a tray with 100 uL 1x SYBR Gold gel stain. Let the gel sit in the staining solution for 30 minutes.

===Imaging the gel===
[[File:PAGE example gel.jpeg|thumb|right| Image of PAGE gel showing single base resolution, ladder on left.]]

Carry the gel tray to the gel imager and carefully place the gel into the imager, centering it on the screen. Set the imager to optimize for faint bands and SYBR Gold staining, and be sure to save the image of the gel that appears.

==Example Procedure==
An example of a PAGE procedure is linked [https://www.overleaf.com/10759609yzcpjjycwjcb#/40396769/ here].

==Resources==
[http://www.bio-rad.com/webroot/web/pdf/lsr/literature/10007296D.pdf Bio-Rad Mini PROTEAN Tetra Cell Instruction Manual]

[https://www.thermofisher.com/us/en/home/references/protocols/nucleic-acid-purification-and-analysis/dna-protocol/pre-cast-denaturing-gels-for-high-resolution-nucleic-acid-analysis.html Thermo Fisher PAGE Guide]

[https://www.nationaldiagnostics.com/electrophoresis/article/denaturing-polyacrylamide-gel-electrophoresis-dna-rna National Diagnostics Denaturing PAGE Guide]

[[Category:Biology]]

Polyacrylamide Gel Electrophoresis

2017-09-12T06:47:26Z

Chao16: Created page with "==Overview== Polyacrylamide gel electrophoresis (PAGE) is a method of separating DNA fragments by length. DNA fragments are loaded into a gel made of many acrylamide polymers...."

File:Gel apparatus.JPG

2017-09-12T06:38:29Z

Chao16: Bio-Rad PAGE gel apparatus and box.

Bio-Rad PAGE gel apparatus and box.

File:Loading dye.jpg

2017-09-12T06:35:10Z

Chao16: PAGE gel image showing loading dye fronts

PAGE gel image showing loading dye fronts

File:PAGE example gel.jpeg

2017-09-12T06:16:44Z

Chao16: Single base-pair resolution on a PAGE gel run at 150V for

Single base-pair resolution on a PAGE gel run at 150V for

2017-09-10T05:36:48Z

Chao16: Created page with "A graphical primer on TdT ==Overview== Terminal Deoxynucleotidyl Transferase (TdT) is a template-independent DNA polymerase, meaning tha..."

File:Tdt infocard.jpeg

2017-09-10T04:53:20Z

Chao16: A Graphical Introduction to Terminal Deoxynucleotidyl Transferase

A Graphical Introduction to Terminal Deoxynucleotidyl Transferase

DNA Synthesizer

2017-09-08T07:07:19Z

Chao16:

[[Category:Biology]]
{{biology-stub}}
Biology Team's Pilot Project: A DNA Synthesizer for Space.

==SSI Biology Pilot Project==
The DNA synthesizer project was started in 2016 as SSI Biology Team's first project. For information on how to join the project, join the SSI Slack and go to the #biology channel. Read information on how to get [[Wet Lab Access]] on this wiki.

==Components of the Synthesis Project==
SSI Bio will be breaking up this DNA synthesizer project into several smaller and more defined subcomponents.

===Enzymatic Synthesis Chemistry===

DNA synthesis is currently done using the [https://en.wikipedia.org/wiki/Oligonucleotide_synthesis#Synthetic_cycle phosphoramidite method], which involves hazardous chemicals and solvents like acetonitrile. Phosphoramidite chemistry is also restricted to centralized synthesis facilities that are hard for scientists in remote locations (like space) to access reliably. Using [[enzymatic synthesis methods]] rather than phosphoramidites would enable small-scale distributed synthesis of short single strands of DNA (oligonucleotides) on the order of 100 base pairs. We are currently working with the enzyme [[Terminal Deoxynucleotidyl Transferase]] (TdT), which has previously been the subject of some prior [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735642/pdf/11693_2009_Article_9023.pdf theoretical work.]

Enzymatic DNA synthesis would be a great alternative way to synthesize DNA in space, for the following reasons:
====Safety, Non-flammability, Non-toxicity====
Most enzymatic reagents could in theory be aqueous solutions, unlike the acetonitrile organic solvents typically used in phosphoramidite chemistry.
====Recyclability, On-Site Reagent Synthesis====
If most of the reagents used are enzymes, then in theory these enzymes could be made by bacteria and then purified on site. This might mean that reagents could be produced, and modified, by the machine itself.

====Improved Speed and Efficiency====
It may be possible that an enzymatic method could improve the speed and efficiency of synthesizing DNA in space. This would be split into two effects. First, being able to make longer strands of DNA would mean that the final product could be composed of fewer parts, which makes the creation of algorithms and strategies for reassembling this DNA to become much easier. Second, being able to make longer strands of DNA faster would cut down substantially on the complexity and time involved with synthesizing DNA.

===Microfluidic Synthesizer Design===
To run a DNA synthesis reaction in a small autonomous payload, we need to precisely move tiny nanoliter-scale amounts of liquid. Microfluidics is a good way to do this. Similar oligonucleotide synthesizers that don't quite fit our needs [http://scholarbank.nus.edu.sg/bitstream/handle/10635/20904/WangC.pdf?sequence=1 have been made in the past]. Good things to know about when designing a device like this: [https://en.wikipedia.org/wiki/Diaphragm_pump diaphragm pumps], [https://en.wikipedia.org/wiki/Solenoid_valve solenoid valves], and of course [https://en.wikipedia.org/wiki/Microfluidics microfluidics in general].

We are currently designing and prototyping an autonomous fluid handling system based on [[Electrowetting on Dielectric]] (EWOD) technology.

===Reassembly Chemistry and Algorithm===
Our oligonucleotides will likely be used directly in downstream applications (as PCR primers, for example), but they could also be put together into biologically functional genes. Most genes of interest are in the ~5,000 basepair range, so current synthesis methods cannot create a gene-length piece of DNA without further processing and assembly. Our assembly chemistry may look something like [https://en.wikipedia.org/wiki/Polymerase_cycling_assembly Polymerase Chain Assembly, also called Assembly PCR].

===DNA Product Verification===
Once a strand of DNA is made, we will need to purify it, check to make sure that it is the correct desired sequence, and purify it for use in downstream applications. This verification can be done a variety of different ways, including [[Polyacrylamide Gel Electrophoresis]] (PAGE), [[Pyrosequencing]], [[Ligation and Sequencing]], or [https://en.wikipedia.org/wiki/Matrix-assisted_laser_desorption/ionization MALDI-TOF Mass Spectrometry].
==Effects of Space on Synthesizer==
===Physical Stress of Launch===
Similar to any other payload, our DNA synthesizer will have to be durable enough to withstand the stresses and forces associated with launch.
===Payload Size and Power Constraints===
We'd like to fit our synthesizer into a 10 centimeter cube, so that it could be launched on and powered by a [https://en.wikipedia.org/wiki/CubeSat CubeSat] as a standardized research payload. To do this, we'll need to design and optimize our fluid handling system, microprocessor, power supply, temperature regulator, and verification technology with size and other constraints in mind.

===Shielding Requirements===
We're not sure what kind of shielding we need! UV radiation can have damage DNA through a process called [https://en.wikipedia.org/wiki/Direct_DNA_damage Direct DNA damage] that can lead to thymine or pyrimidine dimers. This is what causes sunburn, and it's why your skin can tan to help block out UVB.

===Communication from Device===
Depending on our strategy for launching to space, communication from our device to some sort of receiver we can listen to involves a number of interesting questions. How do we return the message that synthesis has been carried out successfully? Will the message describe the sequence of the product created, or a simple boolean yes or no?

==Inspiration and Research==

===History of DNA Synthesizer Idea in SSI===
The idea of a DNA synthesizer for space has been floating around SSI for some time. One of the earliest records stretches back to 2013, in a [[John Cumbers - Synthetic Biology |talk given by John Cumbers.]] John Cumbers was also consulted during the initial conception and planning of the project in the summer of 2015.

Andrew Endy

2017-09-08T06:17:47Z

Chao16: Redirected page to Drew Endy

#REDIRECT [[Drew Endy]]