Sudo Room - User contributions [en]

Talk:Open Biotech/PCR

2013-03-29T00:27:45Z

Hbergeronx: Blanked the page

Compact

2013-03-27T23:03:53Z

Hbergeronx: /* Ratification */

'''For historical purposes and perspectives only. For more info, see [[Sudo room/Compact|the Compact in the context of our old wiki]].'''

'''See the [[Articles of Association]] for current governance documents (like by-laws).'''
=The Compact=
==Ratification==
The compact of members listed below (of at least 23 individuals) agree to the following Articles:

* [[user: Eddankatz|Eddan Katz]]
* The Right Honourable Anthony Di Franco, Chancellor of the Exchequer, Second Lord of the Treasury, Bishop of Ely
* [[user: anca|Anca Mosoiu]]
* ×�×§×¡ ×§×œ×™×™×Ÿ
* marina
* Ryan Bethencourt
* aestetix, with the full backing of [https://en.wikipedia.org/wiki/Emperor_Norton his Majesty Joshua Norton I, Emperor of the United States and Protector of Mexico]
* [[user: HilaryNaylor|Hilary Naylor]]
* Greggawatt Horton and all likenesses herein
* Michael Scroggins
* Victoria
* [[User:Tunabananas|Jenny Ryan]]
* [[User:wrought|Matt Senate]]
* Timon Datatier d'Ã‰ssarviard-Aatenhejm [=Ayer Geisinger Guthrie <name_at_left_outside_brackets>@SRVR.NAME]; 13th Superscriber hereto, hereby, performatively, and by Fiat.
* Jason Euren
* [[User:Karnesky|Rick]]
* [[User:jd|J.D. Zamfirescu]]
* [[User:Juul|Juul]]
* [[User:Deno|Deno]]
* Dan Finlay
* felicia betancourt
* Tracy Jacobs
* Eddie
*Jacob Shiach
* Christopher T Palmer
* Sterling Cooley
* Jae Kwon
* wooster
* davr
* [[User:Yardena|×™×¨×“× ×”]]
* rrix, [http://hackerspaces.org/wiki/staff secretary of defense of hackerspaces.org]
* [[User:Hbergeronx|Hbergeronx]] ([[User talk:Hbergeronx|talk]])

==Articles of Association==
===Article 0. Name===

'''sudo room'''

===Article 1. Purpose===
* '''sudo room''' is an association of individuals (called "sudoers") established to collectively support a [[Sudo_room|creative community and hacker space]] with [[Sudo_room/methodology|corresponding values]].

====Values====
'''sudo room''' is an open, collaborative community of creators and practitioners working toward positive social change. '''sudo room''' chooses to:
#Value open, public discourses over closed, proprietary processes.
#Value access and transparency over exclusivity.
#Value solving real problems over hypotheticals, while respecting visions of the future.
#Value community and collaboration over isolation and competition.
#Value human judgment over automation and efficiency.
#Value do-ocracy over bureaucracy.
#Value safe space over ideology.

===Article 2. Membership===

====Section 2.0 Definition====

'''sudo room''' is a deliberative collective, meaning there is horizontal democratic control and participatory management of the organization, which is composed of all individual members. However, the group actively strives to substantially incorporate interested community participants and beneficiaries who are non-members. Members agree to decisions made by '''sudo room''' as well the terms of these Articles of Association and all future ammendments.

By using spaces or services operated by '''sudo room''', community participants and beneficiaries are obligated to respect all decisions by '''sudo room''' as well as the terms of these articles of association and all future amendments.

====Section 2.1 Qualifications for Membership====

* Membership is defined by fulfilling the following requirements:
*# Contributing monthly dues (sliding-scale with respect to operating costs) or equivalent.
*#* It is an express purpose of the group to keep membership rates low, and therefore accessible, as well as offer, when possible, alternatives to monetary contribution to suffice for monthly dues.
*# A status of good standing with the organization.
*#* Unresolved debts and/or substantial lapses in respecting the values of the organization and its members may result in suspension of membership, to be determined by fair process respecting individual rights and freedoms and the integrity of community norms.

====Section 2.2 Sudo Functionaries====

As a collective, functionary positions are voluntary roles taken on by willing members and intended to change regularly. No person may hold more than one position simultaneously, unless permitted by '''sudo room'''. The positions and respective duties are listed below:
* Facilitator
** Facilitate meetings by maintaining the agenda and ensuring topics are dealt with.
** Can be replaced at any time by some other member through friendly resignation or a simple majority vote. This is a non-confrontational aspect of the role to help facilitation proceed as fluidly as possible.
* Scribe
** Takes notes during meetings, collaborates with others to include their notes in final meeting minutes.
** Posts notes publicly after each meeting
** Can be replaced at any time by some other member through friendly resignation or a simple majority vote. This is a non-confrontational aspect of the role to help note-taking proceed as fluidly as possible.
* Exchequer
** Presents the budget during meetings, as articulated in the budget process below.
** Coordinates with Scribe to ensure budget-related information is accurate with respect to the budget process below.
** Can be replaced at any time by some other member through friendly resignation or a simple majority vote. This is a non-confrontational aspect of the role to help budget-reporting proceed as fluidly as possible.

====Section 2.3 Benefits====

The following are benefits available to all members:
* Usable assets and resources available within reasonable constraints of time and under the condition of sharing.
** '''sudo room''' strives to make assets and resources available to as many non-member participants and beneficiaries as possible.
** Note: no personal property should be stored in '''sudo room''' unless a system for personal storage can be provided by '''sudo room'''.
** Note: the use of '''sudo room''' environments for habitation and/or domestic use is strongly discouraged.
* Approved discounts and services negotiated through the collective purchasing power of '''sudo room'''.
** Items are up to the discretion of '''sudo room''' to determine through its budgeting and decision-making processes.
* A ''safe space,'' which is defined as:
** "A place where anyone can relax and be fully self-expressed, without fear of being made to feel uncomfortable, unwelcome, or unsafe on account of biological sex, race/ethnicity, sexual orientation, gender identity or expression, cultural background, age, or physical or mental ability; a place where the rules guard each person's self-respect and dignity and strongly encourage everyone to respect others." [https://en.wikipedia.org/wiki/Safe-space on Wikipedia].

===Article 3. Decision-Making===
====Section 3.0 Governance====
As a collective, '''sudo room''' members govern themselves and each retains equal rights and mutual responsibilities.
=====Sub-Section 3.0.0 Meetings=====
* Meetings are held regularly, with sufficient notice for interested members to participate.
* A meeting to conduct official business of sudo room must include at least 10 members.

=====Sub-Section 3.0.1 Agenda=====
Agendas will be initiated with a default structure left open to addition until the beginning of the next meeting. Additions to the agenda during the meeting require a simple majority to be added, otherwise they are tabled to the next meeting.

Agenda structure:
# Announcements / Updates
#* '''Decision Procedure:''' Not applicable during meetings.
#* Public announcements may be objected to with timely notice and the burden on the objector.
# Fiscal Solvency (Budget)
#* '''Decision Procedure:''' Automatically approve the budget formed using the procedure outlined below. All amendments to the automatic budget must be made using a consensus process.
# Enforcement / Conflict Resolution
#* '''Decision Procedure:''' ''Fair Process'' described below.
# Proposals for Amendment
#* '''Decision Procedure:''' Follow ''"Amendments" Article '' below.
# Endorsements
#* '''Decision Procedure:''' By consensus.
#* Official '''sudo room''' endorsements of other events, activities, groups, or actions.

====Section 3.4 Enforcement====
=====Sub-Section 3.4.0 Process=====
The resolution of disputes and disagreements within '''sudo room''' is encouraged through informal process and the spirit of a collaborative environment. There is a process, however, by which issues that are not resolved informally and that arise within the scope of these articles of association, should be considered:
# Conflict resolution is attempted through the facilitation of a consenting, neutral, mutually agreed-upon third-party.
# The issue is added to the official '''sudo room''' wiki to be added to the agenda of the next official meeting, save any issues with significant privacy concerns.
# At the beginning of each meeting's agenda item on Enforcement and Conflict Resolution, all unresolved issues on the wiki will be categorized into one of several types. They will be categorized using '''consensus''' and reflecting '''sudo room''''s above values. The categories are (in order of decreasing severity):
## Membership suspension or termination.
##* '''Decision Procedure:''' 2/3 vote
## Safe space.
##* '''Decision Procedure:''' 2/3 vote
## Purely fiscal.
##* '''Decision Procedure:''' 1/2 vote
## Default.
##* '''Decision Procedure:''' Consensus
## Positive feedback.
##* '''Decision Procedure:''' Auto-approval
# The opportunity to represent their perspective is granted to each relevant person, and general discussion may be held about the issue.
# A decision is made by '''sudo room''' to resolve the issue as best as possible, according to the values constituting these articles of association.

=====Sub-Section 3.4.1 Fairness=====
Due process in the resolution of conflicts must include:
# the right to an appeal and a fair tribunal
# the presumption of innocence and the respect for privacy; and
# proportionality and effective remedies.

====Section 3.5 Corporate and Tax Status====

The diversity of organizational structures shall be preserved, in order to maintain the opportunity for the most effective means of instituting incentives for creativity and innovation.

====Section 3.6 Fiscal Solvency====
[https://docs.google.com/spreadsheet/ccc?key=0At_6qzhQZBX8dHU0bWZaNkxpSkcyeG5WMVRwMVQ4aWc#gid=4 FYI, here are the fiscal solvency sheets ya'll]
=====Sub-Section 3.6.0 Assets=====
* '''sudo room''' assets are managed through member benefits above and the budgeting process below.
=====Sub-Section 3.6.1 Budgeting=====
'''sudo room''' employs a transparent, and collaborative budgeting process that attempts to reflect the shared values of all members as articulated by the group's purpose. The budget is located (insert link here). It is managed through the following procedure each month:

# Determine if membership dues can be reduced
# Transparently prioritize budget allocations. (In no particular order) allocate income to match expenditures, contribute to standing funds, and determine remaining surplus
# Any surpluses that remains will be divided based on member contribution and treated as ''internal credits'' (or a ''soft dividend'') available for members to:
## Leave to the discretion of '''sudo room''' to allocate
## Allocate in the budget, at the member's discretion, to various available '''internal projects''' as defined below.
## Provide as future contributions to membership dues.
* '''Note:''' there is a substantial distinction for ''external projects'' as defined below.

* To ensure stability, '''sudo room''' must maintain several standing funds:
** 3 months worth of rent + utilities
** Rainy Day fund (for emergency expenditures)
** Maintenance fund (for necessary infrastructure replacements)
** Operations fund (for necessary, small operational expenditures)

=====Sub-Section 3.6.2 Income=====
'''sudo room''' accrues income through several sources, including events, crowd-funding initiatives, and membership dues.

=====Sub-Section 3.6.3 Dues=====
The recommended monthly dues for members is calculated as follows:
* dues = average over all members of ( 1 month's overhead + a % of any defecit in each standing fund + a risk premium (min. 5% of all other dues components)
** For instance, early on, overhead could be (rent + utilities + services), in which case dues = (500 + 100 + 20 + (10 + 5 + 0 + 10) + 64) / 23 = $30.83 per member

=====Sub-Section 3.6.4 Expenditures=====
* Internal Projects
** Infrastructure, maintenance and improvements.
** Capital Projects
* External Projects
** Not funded this way. Use alternative methods, such as through discounts or crowd-funding opportunities offered as Benefits above.
=====Sub-Section 3.6.5 Surplus=====
'''sudo room''' strives to maintain a zero-sum budget, in which there is no surplus.
* Definition: surplus = income - expenditures - standing funds

===Article 4. Amendments===

====Section 4.1 Process====
The process to ammend these articles of association entails:
# Announcing the proposed amendment, posted:
#* On the official '''sudo room''' wiki.
#* On the '''sudo room''' ''discussion'' email list
#* At least 1 week before the meeting at which a vote on the amendment will be held
# Recieving feedback and commentary posted:
#* On the official '''sudo room''' wiki.
#* On the official '''sudo room''' anonymous etherpad: https://pad.riseup.net/p/sudoroom
#* On any '''sudo room''' email list.
# Adding an agenda item to an official meeting's agenda.
#* The agenda item includes time to review the feedback, recieve in-person feedback, and discuss.
#*'''Decision procedure:''' Consensus

====Section 4.2 Dissolution / Termination of Association====
Dissolution must be proposed in the same manner as all other amendments to these articles. For clarity, the decision procedure will use '''consensus'''.

User:Hbergeronx

2013-03-17T21:29:54Z

Hbergeronx: create intro page

* who are you: matt harbowy
* twitter: @hbergeronx http://twitter.com/hbergeronx
* what do you work on : tea, biotech, programming, science, food, philosophy, human rights
* what do you want to work on: 3d printing, electronics, open source
* what hours do you usually work: weekdays- dayjobbe 7-5. weekends: hacking, writing, coding open source
* if you have a conflict with me, how should you approach me?: in person. if you say "I need some of your time to resolve a conflict", I will work hard to ensure safe space (mentally/physically, as needed) between us and look to find ample time to make things work.
* what resources do you have to offer?: i know more than anyone should know about tea. I have lots of food science/molecular gastronomy tricks up my sleeve. I work in the informatics space at a biotech company and am looking to hack both information accessibility and open source biotech.
* workshops/classes you'd like to lead or have lead in the past: tea and the science of taste.
* what would you want to learn/what classes would you want to take?: 3d printing, basic usage of machine tools, basic electronics
* what else would you like to share about yourself?: I'm the bear that went over the mountain.

Just enough Sketch-up to pretend you can 3d model

2013-03-17T21:13:53Z

Hbergeronx: add "thanks"

[[File:3d 1.jpg|right|thumb]]
[[File:3d 2.jpg|right|thumb]]
[[File:3d 3.jpg|right|thumb]]
[[File:3d 4.jpg|right|thumb]]
==Glance==
*'''WHEN''' 2pm on Saturday the 16th of March.
*'''DURATION''' 2 hours
*'''LOCATION''' [[Getting there|sudo room]]
*'''PRICE''' $0
*'''NUTSHELL''' Live Sketchup and print tutorial
*'''INSTRUCTOR''' Max Klein aka [http://notconfusing.com notconfusing]

==Plan==
*Understand the workflow (Idea>Design>STL>Slice>Print).
*'''IDEA''' a miniature plate for canapes and appetizers that is ring and allows you to hold a drink in the same hand.
*'''DESIGN''' we'll make a 3d digital representation in sketchup
*'''STL''' gloss over this detail and leave it for another class
*'''SLICE''' gloss over this detail and leave it for another class
*'''PRINT''' marvel, and take home.

==Learn==
On the right you'll see some examples of what I've 3D printed at sudo room, having learned all my skills at sudo room, from sudoers.
*Introductions
**Level of 3d modelling experience (none required)
*3D Printing Theory
*Sketchup (many options, but this is easiest, not necessarily most powerful or precise)
**Navigation
***Zoom/Orbit/Pan
***Set views
**Basic Shapes
***Rectangle/Line/Circle/Polygon
***Precise measurements
**Shape Manipulation
***Push/pull
***Move vertice/edge
***Rotate
***Scale
***Scale -1 Trick
***Offset
**Advanced Shapes
***Group
***Follow me
***Outershell
**Misc
***Tape/Erase
**Ready? Let's Make something. Learner's requests?
**Exporting
***[https://github.com/SketchUp/sketchup-stl RBZ File]
*Slic3r slicing software (in a minor way)
**Sometimes can need NetFabb fixing
*Repetier Host Printer Software (in a minor way)
*How to manually adjust the 3d printer in times of crisis.

==Bring==
*Come with a laptop with [http://www.sketchup.com/ sketchup] installed. There's a free version for Windows and Mac. If you don't have this installed, you cannot begin immediately.
*Bring a mouse. Sketchup is much easier with a mouse, and all but impossible to learn with the track pad. Essential.

==Attend==
Add your name below if you know how, but you can also just show up on the day.
* IsThisThingOn
* Tunabananas
* Bleeblahblue
* JustBrandon
* Rick
* Judi (who used the "edit" link, top of the page)
* [[User:Hbergeronx|Hbergeronx]] ([[User talk:Hbergeronx|talk]]) 17:07, 14 March 2013 (UTC) (matt)
* Naomi Sorbet
* Rabbit

==Thanks!==

[[User:Hbergeronx|Hbergeronx]] ([[User talk:Hbergeronx|talk]]) : really enjoyed the class! adding some pics of the "thing" i learned how to sketch up and print, with much help.
<gallery>
File:Sudoroom_prints_toruses.jpg|In progress, finishing top of print
File:Toruses.jpg|translucent quality of PLA plastic
</gallery>
much enjoyed the conversations and sharing of ideas and tools. [[User:Hbergeronx|Hbergeronx]] ([[User talk:Hbergeronx|talk]]) 21:13, 17 March 2013 (UTC)

File:Sudoroom prints toruses.jpg

2013-03-17T21:07:48Z

Hbergeronx:

File:Toruses.jpg

2013-03-17T21:06:33Z

Hbergeronx:

Just enough Sketch-up to pretend you can 3d model

2013-03-14T17:07:43Z

Hbergeronx: /* Attend */

Open Biotech/PCR

2013-02-16T19:06:19Z

Hbergeronx: /* Documentation */

The goal of this project is to build a PCR machine as part of the open biolab. The device should be simple enough that people with a basic skillset can build it on their own while being cheap and simple to produce in a 100x to 500x quantity.

The current target for the entire kit is $300 (PCR, centrifuge, shaking incubator, gel electrophoresis box, micropipette + chemistry/biology/plastics for 3+ experiments). This may turn out to be too low for the first run, but we're aiming at making this as affordable as possible while maintaining a quality that's good enough for day-to-day citizen science work.

= Bill of materials and pricing =

*[https://docs.google.com/spreadsheet/ccc?key=0Akog0JI0-bB9dDA0cTRLWFhlTkVOdGdhSUN4SE5NVEE&usp=sharing#gid=2 Order list for prototype materials]
:Our initial prototype order. Based on aluminum block PCR tube holder. Does not include case.
*[https://docs.google.com/spreadsheet/ccc?key=0Akog0JI0-bB9dDA0cTRLWFhlTkVOdGdhSUN4SE5NVEE&usp=sharing#gid=1 Pricing for between 100 and 500 units unit].
:Some prices estimated. Not including taxes and shipping.

= PCR tube holder =

This is what will hold the PCR tubes. In commercial machines this is usually a block of with holes for the PCR tubes. The holes are usually only deep enough for about 50% of the PCR tube.

Some examples:

*[http://i.istockimg.com/file_thumbview_approve/8677256/2/stock-photo-8677256-pcr-machine.jpg Holy block type]
*[http://thumbs.dreamstime.com/x/polymerase-chain-reaction-%28pcr%29-machine-28261032.jpg Connected cylinders type]

PCR Tube dimensions:

*Height: 20.81 (Â± 0.07) to 20.93 (Â± 0.08) mm
*Diameter: 5.95 (Â± 0.04) to 6.07 (Â± 0.03) mm
:Source: [http://www.spartanbio.com/wp-content/themes/spartan/assets/application_notes/17.pdf Dimensions and thermal property of different PCR tubes]

Note that many PCR machines have PCR tube holes that are much shallower than the height of a PCR tube.

The curvature/slant of the bottom runs to about half-way up the tube.

Three strategies for the PCR tube holder are being investigated:

*Milled aluminum
*Cast pewter
*Air cooling
:Where the PCR tubes are held in a holed piece of wood/plastic/metal.

== Milled aluminum ==

Aluminum has a high thermal conductivity and is easy to machine. Adding a chunk of metal will slow temperature change. This is not desirable for rapid cycling, but it will make it easier to ensure that the temperature at the temperature probe and the temperature in all of the the PCR tubes is the same.

Using a holed sheet of metal and air heating/cooling would be cheaper but may be more difficult to control accurately.

*[http://www.mcmaster.com/#standard-aluminum-sheets/=lfqnfz Aluminum bars from McMaster-Carr]
:1 cm x 4 cm x 6 feet for $35 (enough for 45 4x4 cm tube holders)
:1 cm x 5 cm x 6 feet for $44 (enough for 36 5x5 cm tube holders)
:1 cm x 2.5 cm x 6 feet for $23

Milled aluminum has the problem that a custom-made drill-bit is needed to drill the holes for the PCR tubes. Hackteria has had a few of these made, and will send them to people to loan, but that's not quite as accessible as we would want. Another option is that people can just drill normal holes for the home-made version of the kit and then add a bit of mineral oil to the bottom of the holes to make contact between the PCR tubes and the block of aluminum. We should test how well this works.

== Cast pewter ==

Pros:

*No special drill bit needed (more DIY friendly).
*Metal can be melted on a normal stove.
*RTV silicone mold is re-usable.

Cons:

*Lower heat conductivity than aluminum.
*Molten metal is dangerous.
*RTV silicone mold supplies are expensive.

Supplies needed:

*[http://www.amazon.com/Lyman-Big-Dipper-Casting-Furnace/dp/B0037NA7ZA/ref=sr_1_6?ie=UTF8&qid=1360652567&sr=8-6&keywords=pewter+casting electric casting furnace] $43
*[http://www.amazon.com/Lee-LP90026-Precision-Lead-Ladle/dp/B000LN12Y4/ref=sr_1_1?s=sporting-goods&ie=UTF8&qid=1360653015&sr=1-1&keywords=casting+ladle casting ladle] $12
*high temperature RTV silicone mold kit
*oil-based clay (e.g. chavant)
*lead-free pewter pieces / small ingots

Safety supplies:

*gloves for casting
*face shield
*goggles

= Air cooling =

A sheet of metal with holes in it and a fan to circulate the air.

Controlling the temperature accurately will require more dynamic control but we should try it and see what kind of temperature stability and ramp times we can get.

= Microcontroller =

*Atmega 328
:Same as the standard Arduino
:DIP (through-hole) version is $2.88 but only $1.60 at 100x [http://www.digikey.com/product-detail/en/ATMEGA328-PU/ATMEGA328-PU-ND/2271026 via digikey].
*Atmega 32u4 which has built in USB (meaning that we don't have to include a serial to usb cable)
:No DIP version exists, but QFP version exists which sorta kinda is hand-solderable but not by noobs.
:Price is $3.37 at 100x [http://www.digikey.com/product-search/en/integrated-circuits-ics/embedded-microcontrollers/2556109?k=atmega32u4&quantity=100&ColumnSort=1000011&fid=0 via digikey].

== USB to serial cable ==

*Cables based on the PL2303HX chip can be had for [https://www.google.com/search?q=usb+serial+3.3&hl=en&biw=1024&bih=613&sa=X&ei=8eAaUaiMBMnmiwKd7IHoBQ&ved=0CDIQpwUoAA&tbs=%2Cprice%3A1%2Cppr_min%3A1%2Cppr_max%3A5&tbm=shop&tbo= $3]. Maybe slightly less if we buy in bulk.

= Temperature control =

== Temperature sensing ==

It would be nice to have minimum plus/minus 0.5 C accurate sensors.

Digital is more expensive than analog for an equivalent accuracy, and prohibitively expensive at high accuracy. If we go with the cheaper analog solution then we may have to individually calibrate the sensors.

Arduino ADC resolution is 10 bit, so if hooked up correctly we should be able to get better than 0.2 C accuracy in sampling.

=== Analog ===

*2k ohm NTC thermistor [http://www.digikey.com/product-detail/en/NTSD1XM202FPB50/490-4665-ND/1203944 via digikey] for $0.72 at 1x or $0.37 at 100x.
:About +/- 0.5 C accurate from 0 to 50 C.
:+/- 1.0 C at 75 C.
:+/- 1.5 C at 100 C.
:7.198 k ohm at -5 C.
:0.111 k ohm at 120 C.
*1k ohm NTC thermistor [http://www.digikey.com/product-detail/en/PT103G2/PT103G2-ND/2242426 via digikey] for $1.06 at 100x.
:+/- 0.2 C from 0 to 70 C.
:Min order is 100x.
:Rather minimal datasheet.

We can likely get much better prices for high accuracy thermistors if we are willing to work with SMD components.

=== Digital ===

*Analog Devices TMP36 at [http://www.digikey.com/product-detail/en/TMP36GT9Z/TMP36GT9Z-ND/820404 at digikey] for $1.42 or $1.00 at 100x
:+/- 1.0 at 25 C.
:+/- 2.0 from -40 to 125 C.
*Maxim DS18B20 [https://www.sparkfun.com/products/245 at sparkfun] for $4.25 or $3.40 at 100x.
:1-wire digital sensor.
:+/- 0.5 C accuracy from -55 to 85 C.
:Range is -55 to 125 C.
:12 bit resolution.

== Cooling ==

*Peltier element 40x40 mm [https://www.sparkfun.com/products/10080 at sparkfun] for $15 or $12 at 100x.
:Could not find anything cheaper on digikey.
:It looks like searching for '12709 Tec' can yield small lots of a very very similar device for $5 a piece.

= Heating =

[http://hydraraptor.blogspot.com/2009/01/yet-another-quick-heater-hack.html Using vitreous enamel wire wound resistor]

Use "fire cement diluted with a little water" to hold the power resistor in place. [http://reprap.org/wiki/Geared_extruder_nozzle source].

Maybe use a NIF5003 MOSFET connected to insulated nichrome? [http://forums.reprap.org/read.php?13,51178,55089 source]

Look at extruder controllers:

*[http://reprap.org/wiki/Extruder_Controller_2.2 reprap 2.2 controller]
:Specifically the [http://reprap.org/wiki/Extruder_Controller_2.2#MOSFETS mosfets]

Example [http://energeticforum.com/inductive-resistor/5359-mosfet-heating-circuits.html MOSFET heating circuit].

== Resistors ==

*[http://www.digikey.com/product-detail/en/RS0101R000FE73/RSD-1.0RCT-ND/1166575 10 watt wire wound resistor] at $1.56 or $1.25
*[http://www.digikey.com/scripts/dksearch/dksus.dll?FV=ffec4985%2Cfff40001%2Cfff80482%2C8000a%2C80010%2C8004c%2C8004d%2C80068%2C8006a%2C8006d%2C80075%2C800bc%2C8022a%2C8022b%2C2b8001a&k=resistor&mnonly=0&newproducts=0&ColumnSort=1000011&page=1&stock=1&pbfree=0&rohs=0&quantity=0&ptm=0&fid=0 search for RWM series 8+ watt wirewound resistors] a bit expensive at $4

== MOSFETs ==

*The RFP30N06LE or FQP30N06L [https://www.sparkfun.com/products/10213? from sparkfun] for $1 or $0.76 at 100x. Same price at digikey.
:This has a built in charge pump, which allows it to trigger fully from 3.3v.

Alternatives:

*Digikey page for NIF5003 at $1.37 [http://www.digikey.com/product-detail/en/NIF5003NT1G/NIF5003NT1GOSCT-ND/1967238 here]
:Used in some of the 3D printers for nozzle heater control, but not fully triggerable from 3.3v.
*Jake says, if we want to use "normal" FETs then we can try IXDD604PI

For the simple solution (no heating/cooling in the lid) we need:

*1 MOSFET for regulating heating element.
*1 MOSFET for regulating peltier element.

Each MOSFET needs a [https://www.sparkfun.com/products/11508 10k resistor] and a [https://www.sparkfun.com/products/8589 1N4001 diode] for about $0.30.

== Fans and heatsinks ==

Should be 5 or 12 vdc 5x5 cm. We should use standard CPU coolers since they are cheap an easy to find, which is important since this is the only moving part in the PCR machine and will likely need to be replaced at some point by the user.

*[http://www.digikey.com/product-detail/en/KDE1205PHV2%20MS.A.GN/259-1357-ND/1021206 $4 fan from digikey] - no heatsink included (drops to $2.90 for 100).
*[https://www.sparkfun.com/products/9648 $5 fan from sparkfun] - no heatsink.
*Fan with built in heatsink for $6.20 [http://www.google.com/shopping/product/13394255327842041335?q=cpu%20fan&hl=en&psj=1&bav=on.2,or.r_gc.r_pw.r_qf.&bvm=bv.42261806,d.cGE&biw=1024&bih=613&sa=X&ei=SvkZUamMBaKsjAKMhYDwAQ&ved=0CH8Q8wIwAA&prds=scoring:tp via google]
*Fan with built in heatsink, but a bit too big for $5.00 [http://www.outletpc.com/c1987.html?utm_source=c1987&utm_medium=shopping%2Bengine&utm_campaign=googleproducts via outletpc.com]

We also need a transistor to control the fan. The digikey fan uses 0.8 watt and the sparkfun fan uses 1 watt.

Assuming the fans are 12 volts, the NPN 2N3904 can be used (but it's max 200 mA) [https://www.sparkfun.com/products/521 via sparkfun] at $0.75 but they're less than 10 cents at 100x.

= Power supply =

*12v 10amp [http://www.amazon.com/Logisys-Corp-Bearing-Supply-PS550E12BK/dp/B004MU8VCS/ref=sr_1_2?ie=UTF8&qid=1360655541&sr=8-2&keywords=atx+power+supply power supply] $24, but can be used for centrifuge and incubator as well.

*24-pin ATX PSU female [https://www.sparkfun.com/products/9498 connector] and [https://www.sparkfun.com/products/9558 breakout-board] for $7 total.

*[http://www.mouser.com/ProductDetail/Molex/44206-0007/?qs=g5f4E6w8l8gzEjxCgQ0R8g%3D%3D&gclid=CJar6Je-srUCFeeDQgodPBYAgA via mouser] for $0.74 or x100 for $0.65

= Previous work =

== Existing DIY cyclers ==

*[http://openpcr.org/ openpcr]
*[http://russelldurrett.com/lightbulbpcr.html lightbulb pcr]
*[http://www.instructables.com/id/Arduino-PCR-thermal-cycler-for-under-85/?ALLSTEPS Arduino PCR]
*griessen pcr
*[http://pimm.wordpress.com/2009/10/31/lavaamp-cheapest-pocket-pcr-thermocycler-dreamed-for-diy-biologists/ lava-amp]

*[http://diyhpl.us/~bryan/papers2/microfluidics/2010-01-20/Petri%20dish%20PCR%20-%20laser-heated%20reactions%20in%20nanoliter%20droplet%20arrays.pdf laser-heated petri dish PCR]
*[http://144.206.159.178/ft/943/73743/1264824.pdf A portable battery-operated chip thermocycler based on induction heating]

== Useful links ==

* [http://hackteria.org/wiki/index.php/Jugaad_PCR_Thermocyclers Hackteria PCR notes]
* [http://openwetware.org/wiki/DIYbio:Notebook/Open_Thermal_Cycler DIYbio:Notebook/Open Thermal Cycler]
* [http://russelldurrett.com/lightbulbpcr.html The Light Bulb PCR Machine]
* [http://groups.google.com/d/topic/diybio/XqIJ3l-IHZ8/discussion $10 buck thermocycler design work]
* [http://groups.google.com/d/msg/diybio/r7opEnSApkU/arffsaDtv_oJ Re: inexpensive PCR designs UnBlockedâ„¢]
* [http://groups.google.com/d/topic/diybio/ZzMZohMpgB8/discussion The open-source Pacer PCR]
* [http://groups.google.com/d/topic/diybio/tlPUBoCTf-Q/discussion Cheaper OpenPCR]

= Documentation =

== Peltier ==

I've been looking at the specs of some Peltier chips (see https://docs.google.com/file/d/1u2m--LONYCOyvcp76spoAP3wN3nWroROwfTtoJx9TpeeeMYY1WVNb1-KCXOk/edit?usp=sharing ) and on some of them, they seem to be designed for lower temperature operation and the lifetime of the device will be significantly reduced if you operate them at a high temperature (the limits of the device in the attached spec device, for example, is 80C.) At 95C, the hot side quickly ramps up from the cold side temp, which is starting at 95C, I've heard as much as 4x the rate of the cold side. By the time you got to 80C on the cold side, you could easily exceed 150C if your heat sink isn't able to pump that much heat that quickly.

I think to ensure against damage or reduced life, you have to carefully control the amount of volatge/current applied. A feedback loop to limit applied voltage based on temp of hot side seems to be a sensible addition. I'm still trying to figure this out for a temperature controlled minielectrophoresis unit that I am designing (to be open source). A cheap unit becomes not so cheap if after a handful of runs, you have to fix it: not trying to imply that you haven't thought of this or to be a downer, but just raising awareness of something that only recently came to my attention.

== MOSFETs ==

*[http://bildr.org/2012/03/rfp30n06le-arduino/ bildr tutorial]
*[http://www.sparkfun.com/news/819 20 min video about MOSFETs]

= Protocols =

== DNA extraction ==

http://www.scq.ubc.ca/the-macgyver-project-genomic-dna-extraction-and-gel-electrophoresis-experiments-using-everyday-materials/

== Transformation ==

[http://hackteria.org/wiki/index.php/GFP_Protocol_Jugaad GFP]

== Electrophoresis ==

[http://learn.genetics.utah.edu/content/labs/gel/electrophoresis/ University of utah's guide]
[http://www.instructables.com/id/How-to-Prepare-an-Electrophoresis-Argarose-Gel/step3/Cast-the-Gel/ How to prepare a gel]