brmlab project:biolab

Sterilizátor

Anonymous (anonymous@undisclosed.example.com) — 2016-10-12T16:14:17+00:00

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	Suroviny:		Suroviny:
	* Destilovaná voda		* Destilovaná voda
-	* Elektřina (~230V@50Hz)	+	* Elektřina (~230V@50Hz) Minimálně 15A, ne do prodlužky!
	* Cas (cca 45 min)		* Cas (cca 45 min)

	Zapnutí:		Zapnutí:
	- Zapoj autokláv do elekřiny		- Zapoj autokláv do elekřiny
		+	- Nahod modry jistic na zadnim panelu
	- Zapni ho (zelený přepínač na předním panelu)		- Zapni ho (zelený přepínač na předním panelu)
	- Doplň destilovanou vodu do díry "Clean water tank"		- Doplň destilovanou vodu do díry "Clean water tank"

BioBox

Anonymous (anonymous@undisclosed.example.com) — 2016-11-10T15:02:06+00:00

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	==== Dokumentace ====		==== Dokumentace ====

-	Příruby k rukavicím jsou v deskách Technická dokumentace (Top Secret), elektronická verze.	+	Příruby k rukavicím jsou v deskách Technická dokumentace (Top Secret), elektronická verze nejde uploadovat (TODO).

BioOSM

Anonymous (anonymous@undisclosed.example.com) — 2019-09-20T19:14:04+00:00

	current
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	+	====== BioOSM ======
	+	{{template>:project:infobox\|
	+	name=Biologicke zbrane ve vasem okoli\|
	+	image= bioosm:bioosm.jpg?400 \|
	+	founder=[[user:sachy]]\|
	+	interested=[[user:sumie-dh]]\|
	+	sw=CC-BY-SA\|
	+	hw=N/A\|
	+	status=active}}
	+	~~META:
	+	status = active
	+	&relation firstimage = :project:bioosm:bioosm.jpg
	+	~~

	+	~~REDIRECT>:project:bioosm:start~~

BioStrike: Open Antibiotics Discovery

Anonymous (anonymous@undisclosed.example.com) — 2014-05-04T01:02:07+00:00

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	+	====== BioStrike: Open Antibiotics Discovery ======
	+	{{template>project:infobox\|name=BioStrike\\ Open Antibiotics Discovery\|
	+	image=biostrike.jpg?200\|
	+	founder=[[user:denisakera]]\|
	+	interested=[[user:denisakera]]\|
	+	status=active\|
	+	}}

	+
	+
	+	//Dedicated to Albert Schatz, who discovered streptomycin and saved millions from tuberculosis, our Nobel prize martyr-laureate. This project is trying to purify science through soil bacteria, which we hope will return research to people like him and find cure against big pharma greed.// Read the story of [[http://www.theguardian.com/books/2012/jun/29/experiment-eleven-tuberculosis-peter-pringle-review\|Experiment eleven]]
	+
	+	Global open biology project supporting the ideals of open science, in which we screen soil bacteria, such as Actinomyces, Streptomyces and Micromonospora for antibiotic properties and to explore the user experience of sharing and discussing open data. It is initiated by DIYbio Waag in 2012 during the first DIYBIO Europe meeting in Paris (Dec 2012) and developed into a global project in October 2013 during a workshop in the Lorentz center in Leiden. It is a part of larger DIYBIO Europe project called BugID on bioprospecting of soil bacteria. The implementation started in October 2013 in a workshop called Innoculab session, by the Waag Society Open Wetlab and BiologiGaragen during the Re-new Festival in Copenhagen [[http://biologigaragen.org/renew/\| Biologigaragen]].
	+
	+	Antibiotics have saved millions of lives over the last century. However, many microbes have evolved new mechanisms to withstand these once powerful medicine.
	+
	+	Participate in the BioStrike challenge to hunt for new antibiotics and learn about microbiology starting in your own backyard and kitchen.
	+
	+	There are microbes all around us and everywhere on the planet. They are constantly competing and battling to survive and evolve. Some microbes produces compounds that are toxic to other microorganisms, and these compounds can be used as antibiotics in medicine. The microbes and antibiotics are different all over the world and also depending on what the microbes are growing on, what medium. We invites individuals, high schools and communities to participate in the search for new antibiotic producing microorganisms. It’s up to the participants to find the optimal conditions and measure the capability of their strain to inhibit the growth of the reference strain. The results and strains will be collected and ranked on a global ladder. The data will be openly peer-reviewed by the organizing community.
	+	==== Goals ====
	+	A fun gamified competition and participatory community
	+
	+	Open participatory experiential learning
	+
	+	Low barrier to enter the challenge, but a potential of a gradually increasing learning curve as the participants progresses
	+
	+	Global scientific collaboration
	+
	+	Potential of discovering new antibiotics through Open drug discovery
	+
	+	There is an ongoing discussion on the hierarchy of goals in this project: bioprospecting, education, engagement, science communication, open science rituals & interpretation of science history, bioart- citizen science experiment. Pieter offered a good summary: "To me, it's more about engagement and education. You never know what you might find in the process. Just working with microbiology is an exciting to many people in itself. The project has a low entry level, and encourages collaboration, discussion and self education. It can be done as a workshop in groups, or by individuals in many different settings. It could be a nice answer to the many "where do I start"-topics on the global DIYBio discussion group, as it offers a guideline along which one learns what materials and equipment need to be acquired for what purpose. Furthermore, it explores the infrastructure that is needed to set up a true international collaborative DIYBio project, ultimately leading the way towards open drug discovery. Although the likelihood of finding a new antibiotic may be theoretically slim, it might be that this project will breed a new generation of scientists that will actually achieve that goal."
	+	==== Status ====
	+
	+	==== Phase 1: Defining the Protocol ====
	+
	+	Google Drive [[https://drive.google.com/#folders/0BzADIb9rSQQ3WTI4Z0pWOGl2bzg\| Results of the first workshop in Copenhagen]]
	+
	+	Synbiota collaboration on the protocol [[https://synbiota.com/projects/328/workspace_pages\|Protocol Discussions]]
	+
	+	Zotero links for articles [[https://www.zotero.org/groups/biostrike/items\|Links]]
	+
	+	Google group discussion [[https://groups.google.com/forum/#!forum/biostrike\| General discussion]]
	+
	+	==== Science Issues ====
	+
	+	Biosafety issues [[http://ask.diybio.org/questions/under-what-conditions-can-i-generate-bacterial-isolates-from-environmental-samples-in-bsl1-lab/\|Isolating bacteria from soil]]
	+
	+	How to train people outside of a lab to understand and take proper measures against the health risk of dealing with soil isolates, such as Aspergillus mold?
	+
	+	1. Train people in professional microbiology safety procedures and building a BS2 lab. Maybe in collaboration with microbiology department and DIYbio labs in hackerspaces.
	+
	+	2. Designing the growth medium properly: Streptomyces selective medium preventing the growth of other organisms (mix the medium with antifungal cream?), treating the sample with heat (Streptomyces spores are mildly heat resistant, many other bugs are not).
	+
	+	3. Define basic rules, such as "You do not inhale and touch anything that grows on the plate" or "You dispose the medium by cooking it for x minutes under x temperature"
	+
	+	Logic behind this: "BSL1 restrictions are too abstract and not useful for an the average amateur. How is growing plates with diluted mud any different from leaving your dinner leftovers in a bin for 2 weeks at room temperature? The idea behind this project is to join the forces of science and people, not turning everyone into scientists."
	+
	+	Basic rules: wearing gloves so you don't contaminate your plates with human pathogens, incubating at room temperature rather than body temperature, working underneath a tupperware box to provide a bit of a physical barrier to contamination, etc.
	+
	+	October 2013 guidelines [[https://docs.google.com/document/d/1lBJiI6WkWHJap-0MfxHXmXXYhBLl8-kbARiM11iQTws/\| Roskilde document]]
	+
	+	Original guidelines [[http://www.diybio.eu/community-biolab-safety-guidelines/\|DIYbio EU guidelines]]
	+
	+	Evaluation of antibiotics
	+
	+	How to increase the chance of discovering some novel antibiotics?
	+
	+	Streptomyces have been mined for antibiotics for decades, how to bias the selection in favour of novel parts of the antibiotics spectrum?
	+
	+	How to support inexpensive way to screen tons of isolates, characterize their antibiotics, and identify the novel ones?
	+
	+
	+	==== Phase 2: Design of Interaction over Agar Plates ====
	+
	+	==== Design Issues ====
	+
	+	1. The challenge is to use agar plates with inhibition zones from various locations to motivate people to take a lot of samples and share.
	+	Should it be a hunt, adventure, tournament, cross-platform (mobile, online, offline)?
	+
	+	2. What if the whole process is a form of science purification ritual, returning innocence to science against big pharma money industry? Connection with our soil is full with symbolic meaning, which we can use for some interaction ideas. Should we add this more "serious" dimension to the activities, so people get diploma with special bacterial ink or other paraphernalia related to being motivated friends of good bacteria or something? Helping science to remain open one bacteria per time?
	+
	+	3. Infographics explaining and helping the amateurs to work with agar plates and practice basic science protocols & safety.
	+
	+
	+	=== User Experience ideas ===
	+	How to use game elements (collecting, badges, tournaments)?
	+
	+	How to turn the images of inoculated plates and the zones of growth inhibition into game mechanics or some novel user experience?
	+
	+	1. Badge or Pokemon style collection with various "killers" in forms of photos, people name their agar plates/strains
	+
	+	Typical Badge Model [[http://scistarter.com/blog/2013/10/gamifying-citizen-science-floracaching/\|Florcaching]]:
	+
	+	Badges associated with particular activities are placed on the virtual profile pages of users. Each badge is linked to an activity that has been identified as a motivation for gamers: fun, community involvement, competition or personal performance. For example, the Invasive Patroller badge requires users to create a cache of an invasive species, and the Friendly Floracacher requires players to check in with another person. Some of our badges relate to collecting a certain number of different plants, uploading images of plants that the Encyclopedia of Life needs photos of, validating the identification of other people’s caches, and being the first to find a new species...
	+
	+	Challenges in the badge model [[http://gamification-research.org/wp-content/uploads/2013/03/Bowser_Hansen_Preece.pdf\|Gamification of Citizens science issues]]:
	+
	+	How can gamified apps be built to appeal to an audience that enjoys game-like interfaces, and an audience that may find them distracting?
	+
	+	How can gamification enhance the experience of an audience that already displays powerful intrinsic motivations?
	+
	+	How should gamified apps be modified when supporting data quality is a crucial task?
	+
	+	It seems like the badge model is good for supporting activities you do for the first time, but how good is it for tedious, everyday work? Maybe collections are better model for that, like collections of plates representing various strains and building something of an army.
	+
	+
	+	2. Tournaments: every month the two strongest strains will compete and it is documented as stop animation
	+
	+	3. Cross-platform interaction
	+
	+	Actions of the microbes change some virtual world, people create their own narrative under certain mechanisms/systems/worldviews, people can win prizes from bioartist, so we connect citizen science with bioart.
	+
	+	Simon Park has a nice piece on textiles with Streptomyces [[http://exploringtheinvisible.com/2012/11/13/biogenic-designs-patterned-panacea/]], maybe some fashion items from the most successful strains, which we will identify? The textiles infused with such bacteria have a forest soil smell and nice colours, velvety feeling.
	+
	+	4. Soil rituals
	+	[[http://en.wikipedia.org/wiki/Ritual_purification]]
	+
	+	=== APIs ===
	+	How to integrate the various services with Synbiota?
	+
	+	Define API requirements for Synbiota.
	+
	+	==== Phase 3: Impact ====
	+	How to sequence the successful strains?
	+
	+	Cooperation with some big sequencing company?
	+
	+	Metagenomic analysis and more open search for bacteria?
	+
	+
	+	==== Legal Issues ====
	+	What licences to use in Open Science?
	+	Proposal [[http://creativecommons.org/licenses/by/3.0/]]
	+	==== Research Questions ====
	+	How can citizen science support open science and vice versa?
	+
	+	What collaborative mechanisms and user experience design strategies can improve sharing, crowdsourcing and discussing of data?
	+
	+	How to support open drug discovery with gamification, crowdsourcing and user experience design?
	+
	+	How to manage issues of biosafety, standardization of protocols and quality control on a global level?
	+
	+	What are the opportunities and issues in involving amateur and professional actors and stakeholders in the various stages of the project?
	+
	+	What roles can CC and similar open licenses play in open drug discovery?
	+
	+	How such project supports science communication and education, public participation in science and policy deliberation, but also the actual production of scientifically valuable data?
	+
	+
	+	==== Documentation ====
	+
	+	[[https://dl.dropboxusercontent.com/u/1526632/BioStrike.odt\|Original BioStrike.odt proposal 2012]]
	+
	+	[[http://exploringtheinvisible.com/2013/03/22/bioprospecting-for-art-antibiotics-and-cancer-cures/\|Simon Park Biprospecting proposal 2013]]
	+	Despite this, the number of new antimicrobial compounds reported to have been isolated from this group has declined in recent years and is predicted to fall to zero in the next 1-2 decades. The Streptomyces, as a group, are predicted to be capable of producing at least 100,000 antibiotics, and only a minute fraction of this therapeutic diversity has been unearthed so far.
	+
	+	[[http://hackteria.org/wiki/index.php/Actinomycetes_Tournament:_Open_antibiotics_discovery\| Lorentz center proposal 2013]]
	+
	+	[[http://www.flickr.com/photos/mmborch/sets/72157635011047084\|Labitat Re-new digital arts festival Makerspace 2013]]
	+
	+	[[https://www.flickr.com/photos/pietervanboheemen/tags/plate/\| October 2013 Re-new digital arts festival Agar plates]]
	+
	+	[[https://docs.google.com/document/d/1LjZCaKrbu-dARUsQSFd522tgcuBanYjdTwPT9mQpaAY/\|Summary October 2013 Roskilde Festival]]

BrmHistology

Anonymous (anonymous@undisclosed.example.com) — 2017-09-20T23:01:23+00:00

	current
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	+	====== BrmHistology ======
	+
	+	{{template>project:infobox\|
	+	name=BrmHistology\|
	+	image=nahled.jpg?400\|
	+	founder=[[user:sumie-dh]]\|
	+	interested=[[user:sachy]]\|
	+	status=active
	+	}}
	+
	+	~~META:
	+	status = active
	+	&relation firstimage = :project:projectlogo.png
	+	~~
	+
	+	Uz pres rok rezeme zivocichy [mrtve, zivi se prilis hemzi] na platky a menime prirozene bezbarve tkane na 50 odstinu fialove/ruzove ;]
	+
	+	==== Technika ====
	+
	+	===Mikrotomy===
	+
	+	== Mikrotom sankovy==
	+
	+	{{http://www.sumie-dh.cz/images/gallery/mikrotom2.jpg?direct&400}}
	+
	+	Pro presnejsi histologickou praci stoji na mikroskopovacim stole mikrotom Meopta 596 C8. Je to poradny kus kovu, prosime nepresouvat ;] Nuz je k dispozici na vyzadani pote co bude zajemce obeznamen s funkci pristroje, bez toho je velice snadne se nozem zranit nebo ho znicit [popripade oboji].
	+	Mikrotom je vhodny pro rezani tkani zalitych do parafinu, tloustka rezu je nastavitelna do 3 um.
	+
	+	PS: tento pristroj neni hackable, je to jedna z tech veci kterou nelze prilis obejit DIY projektem, je potreba poctivy kus tezkeho zeleza ;]
	+
	+	PPS: pokud uz mate opravdovy mikrotom, lze s nim provadet drobnejsi hacky, napr. pokud je potreba prichladit vzorek [parafin se krouti, lame v teple mistnosti], hodi se Peltieruv clanek
	+
	+	{{http://www.sumie-dh.cz/images/gallery/peltiersedi.jpg?direct&400}}
	+
	+
	+	== Mikrotom [rucni] ==
	+
	+	owner: [[:user:pinky\|pinky]]
	+
	+	[[https://brmlab.cz/lib/exe/fetch.php?tok=36b318&media=http://www.sumie-dh.cz/images/gallery/mikrotom.jpg\|{{http://www.sumie-dh.cz/images/gallery/mikrotom.jpg?direct&400}}]] [[https://brmlab.cz/lib/exe/fetch.php?tok=d96fa6&media=http://www.sumie-dh.cz/images/gallery/mikrotom-nuz.jpg\|{{http://www.sumie-dh.cz/images/gallery/mikrotom-nuz.jpg?direct&400}}]]
	+
	+	Pocitejte s tim ze u tohoto mikrotomu nedosahnete kvality kterou vetsina skutecne histologicke prace vyzaduje, vzdy dostanete vzorek na nemz bude videt nekolik vrstev bunek, pri barveni budete videt "orvane" okraje tkani, ktere se barvi ochotneji nez u spravne rozvnomerne provedeneho rezu.
	+	Je ale dostacujici na nektera pozorovani rostlinnych pletiv a tkani, ktere maji transparentnejsi charakter [napr. tuk nebo chrupavky]. K mikrotomu patri mikrotomovaci nuz [je mozno nahradit ziletkami, pokud zjistite ze je nuz tupy a nemate odvahu jej brousit].
	+
	+	Princip prace s mikrotomem je videt nize na videu [popripade si chytte [[:user:sumie-dh\|sumie-dh]], ukaze vam to pokud si nejste jisti].
	+
	+	{{youtube>uB-acKfWlV4?medium}}
	+
	+	\\
	+	\\
	+
	+	=== Mikroskopy ===
	+
	+	...maji vlastni [[equipment:brmicroscopy\|wiki]] ;]
	+
	+	=== Histologicke barvicky ===
	+
	+	Aktualne disponujeme slusnou paletou barviv vhodnych pro mikroskopii. Podivejte se co se schovava v [[http://brmko.brm/chemlab.html\|http://brmko.brm/chemlab.html]] pod tagem barvivo. Pokud najdete pozadovanou barvicku jako roztok, je doporucovany postup jej pouzit misto vyroby noveho roztoku. Barvicky jsou drahe a spousta protokolu ktere najdete "nekde na internetu" nefunguji tak jak by mely. Konzultujte nejen techniku, ale i pouzitou chemii s chemlabaky , napr s [[:user:pinky\|pinky]], je mozne ze lze pouzit chemii setrnejsi k pozorovateli a cene procedury.
	+
	+	=== Drobne potreby vhodne k priprave vzorku ===
	+
	+	Muze se hodit:
	+
	+	Preparacni sada [pinzety, preparacni jehly, ocni nuzky]\\
	+	500ml topne hnizdo + sklenena misticka na vodu vhodna na natahovani rezu\\
	+	Velka hodinova skla pro zachytavani nepovedenych rezu\\
	+	Stetce pro cisteni mikrotomu\\
	+	Sklenene desky vhodne jako podlozka pri montovani rezu\\
	+
	+	=== Drobne 3D modely ===
	+
	+	Nektere veci mame jiz namodelovane pro 3D tisk, vyhneme se tak efektu 'lze koupit pouze v baleni po 500ks'. Zalevaci komurky je vhodne tisknout z tepelne odolnejsiho plastu, napr PET. Vetsina plastu
	+	pouzivanych v 3D tisku se nekamaradi s prosvetlovacimi rozpoustedly [benzen, toluen, xylen].
	+
	+	Zalevaci komurky [base molds]
	+
	+	[[http://www.sumie-dh.cz/data/files/dock.stl\|mrnave vzorky]]\\
	+	[[http://www.sumie-dh.cz/data/files/38-29-10.stl\|male vzorky]]\\
	+	[[http://www.sumie-dh.cz/data/files/jicen.stl\|stredni vzorky]]\\
	+	[[http://www.sumie-dh.cz/data/files/jicen-vetsi.stl\|velke vzorky]]\\
	+
	+	Histologicke kazety [male]
	+
	+	[[http://www.sumie-dh.cz/data/files/cassete-v2.stl\|vrsek]]\\
	+	[[http://www.sumie-dh.cz/data/files/cassete-spodek3.stl\|spodek]]\\
	+
	+	Kosticky do mikrotomove svorky > dobre nam funguji [[https://www.thingiverse.com/thing:955078\|LEGO kostky]] ;]\\
	+	Nastavitelne boxiky na [[https://www.thingiverse.com/thing:1416590\|zamontovane vzorky]]
	+
	+	==== Barvici protokoly ====
	+
	+	Z hovoru s odborniky s praxi z oboru vyplynulo ze internet neni prilis dobrym zdrojem spolehlivych protokolu.
	+	Proto postupy prebirame ze skripta Histologie a histologická technika II od Zdenka Vacka. Oba dily velmi pravdepodobne najdete v biolabi knihovne.
	+
	+	V biolabu se pouziva odvodnovani alkoholovou radou, prosvetlovani toluenem a zalevani do parafinu [Paraplast s ruznou teplotou tani]. Mame DYI verzi vodni lazne pro parafinovani a termostat pro
	+	natahovani parafinovych rezu na sklicko.
	+	Montuje se do Eukittu kvuli jednoduchosti [odpada nutnost vracet rezy zpet do termostatu kvuli tvrdnuti kanadskeho balzamu].
	+
	+
	+	Vyzkouseli jsme a fungovalo:
	+
	+	Eosin-Hematoxylin\\
	+	Nisslovo barveni\\
	+	Grammovo barveni\\
	+	Bielschowskeho protokol [nervove fibrily]
	+	Fuchsin [barveni rostlinnych pletiv]
	+
	+
	+	==== Vysledky ====
	+
	+	Mame v supliku nekolik vzorku v koukatelne kvalite [casem dostanou vlastni wiki] :
	+
	+	__Savci__
	+
	+	[[http://www.sumie-dh.cz/images/gallery/deloha-s.jpg\|Deloha [Prase domaci]]] \\
	+	[[http://www.sumie-dh.cz/images/gallery/esophagus-pano1.jpg\|Jicen - [Prase domaci - prurez]]] \\
	+	[[http://www.sumie-dh.cz/images/gallery/uzlina.jpg\|Mizni uzlina - [Tur domaci]]] \\
	+
	+	__Ptaci__
	+
	+	Jicen [Kachna domaci] \\
	+
	+	__Ryby__
	+
	+	[[http://www.sumie-dh.cz/images/gallery/pyloric-region.jpg\|Zaludek [Tetra paraquayska - Moenkhausia sanctaefilomenae]]]\\
	+	Strevo [Tetra paraguayska - Moenkhausia sanctaefilomenae]\\
	+	[[http://www.sumie-dh.cz/images/gallery/vajca21.jpg\|Vajecnik [Tetra paraguayska - Moenkhausia sanctaefilomenae]]]\\
	+	Rez koronarni [Zivorodka endlerova - Poecilia wingei ♀]\\
	+

project:biolab:centrifuge-scad

Anonymous (anonymous@undisclosed.example.com) — 2012-05-12T02:24:34+00:00

1336789443	current
Line 1:	Line 1:
	+	<code>
	+	// ===== DremelFuge =====
	+	// Cathal Garvey (cathalgarvey gmail com
	+	// Creative Commons NonCommercial Sharealike Attribution license
	+	// http://creativecommons.org/licenses/by-nc-sa/3.0/

	+	// ===== Parameters =====
	+	// Includes:
	+	<shapes.scad><Eppie.scad>
	+	// Note: Shapes.scad is released under a GNU License, further details in that script.
	+	// Many thanks to Catarina Mota <clifford@clifford.at> for providing this very useful resource to the community!
	+	// Note also: Eppie.scad is released under a Creative Commons Attribution Sharealike License.
	+
	+	// All dimensions are in mm.
	+	// $fn is a global variable that determines the number of faces to divide a curved surface into. Increase $fn for more detailed models.
	+	$fn = 70;
	+
	+	// EppieRad is how wide the top of the eppie is, but not the lip! The Lip should exceed this width by a good margin!
	+	EppieRad = 5.35;
	+	EppieLipRad = 6.65;
	+	// AxleRad is the radius of the axle that protudes from the top, which is accepted by the drill/dremel to spin the device.
	+	// AxleLength is how long the Axle is, including the rotor.
	+	AxleRad = 4.5;
	+	AxleLength = 12.5;
	+	HollowAxle = 1;
	+
	+	// AxleInnerRad is how wide the inner bore of the axle should be, if HollowAxle is set to 1.
	+	// AxleInnerDepth is how deep the bore should be starting from the top of the Axle Length.
	+	// ScrewHoleRad is how wide the smaller hole at the end of the Inner Bore should be.
	+	AxleInnerRad = 2.45;
	+	AxleInnerDepth = 10.5;
	+	ScrewHoleRad = 1;
	+
	+	// RotorDisplacement is how far from the central axle the rotor is intended to extend.
	+	// This determines in large part the G-force that will be applied to the spun samples.
	+	RotorDisplacement = 40;
	+	// RotorEdgeSpan is how thick the rim of the rotor should be.
	+	// This confers strength and momentum, but puts more strain on the dremel and likely increases the odds of uneven plastic infill.
	+	RotorEdgeSpan = 5.8;
	+	// SpokeWidth is how thick the spokes of the rotor/axle are.
	+	SpokeWidth = 3;
	+	// SpokeSpan is how long a spoke is from tip to tip.
	+	SpokeSpan = RotorDisplacement*2 - RotorEdgeSpan / 2;
	+
	+	// RotorHeight is how tall the Rotor is when placed on end. It's important that this be larger than the diameter of the Eppies used, or the holes cut for the Eppies will be larger than the rotor's rim!
	+	RotorHeight = 17; //was: 12.5
	+
	+	// ===== Modules ======
	+	module Spoke(SpokeH,SpokeL,SpokeW,SpokeRo){
	+	translate([0,0,SpokeH/2]) rotate([0,0,SpokeRo])
	+	cube([SpokeL,SpokeW,SpokeH],center=true);
	+	}
	+	module Rotor(SpurR,SpurH,RimW,RimR,SpokeW,Height,BoreD,BoreW,ScrewW){
	+	difference(){
	+	union(){
	+	cylinder(SpurH,SpurR,SpurR);
	+	tube(Height,RimR,RimW);
	+	Spoke(Height,SpokeSpan,SpokeW,60);
	+	Spoke(Height,SpokeSpan,SpokeW,120);
	+	Spoke(Height,SpokeSpan,SpokeW,180);
	+	}
	+	if(HollowAxle == 1){
	+	translate([0,0,SpurH-BoreD]) cylinder(BoreD,BoreW,BoreW);
	+	cylinder(SpurH,ScrewW,ScrewW);
	+	}
	+	}
	+	}
	+	module EppieCutouts(CutOutSize,Rotation){
	+	// Cylinder for Eppie:
	+	translate([0,0,0.75*RotorHeight]) rotate([0,90,Rotation]) translate([0,0,-RotorDisplacement-1])
	+	cylinder(RotorEdgeSpan+3,CutOutSize,CutOutSize);
	+	translate([0,0,0.75*RotorHeight]) rotate([0,90,Rotation])
	+	translate([0,0,-RotorDisplacement+RotorEdgeSpan-0.5])
	+	cylinder(3,CutOutSize+1.2,EppieLipRad);
	+	// Box cutout for ease of insertion:
	+	translate([0,0,RotorHeight-2]) rotate([0,90,Rotation]) translate([0,0,-RotorDisplacement+3.7])
	+	cube([5,CutOutSize*2-0.48,RotorEdgeSpan+2],center = true);
	+	// Box cutout to preserve cap closure:
	+	translate([0,0,1.9]) rotate([0,90,Rotation]) translate([0,0,-RotorDisplacement+RotorEdgeSpan])
	+	cube([4,CutOutSize*2-0.5,4],center = true);
	+
	+	// Matching Cylinder for facing Eppie:
	+	translate([0,0,0.75*RotorHeight]) rotate([0,90,Rotation+180]) translate([0,0,-RotorDisplacement-1])
	+	cylinder(RotorEdgeSpan+3,CutOutSize,CutOutSize);
	+	translate([0,0,0.75*RotorHeight]) rotate([0,90,Rotation+180])
	+	translate([0,0,-RotorDisplacement+RotorEdgeSpan-0.5])
	+	cylinder(3,CutOutSize+1.2,EppieLipRad);
	+	// Box cutout for ease of insertion:
	+	translate([0,0,RotorHeight-2]) rotate([0,90,Rotation+180]) translate([0,0,-RotorDisplacement+3.7])
	+	cube([5,CutOutSize*2-0.48,RotorEdgeSpan+2],center = true);
	+	// Box cutout to preserve cap closure:
	+	translate([0,0,1.9]) rotate([0,90,Rotation+180]) translate([0,0,-RotorDisplacement+RotorEdgeSpan])
	+	cube([4,CutOutSize*2-0.5,4],center = true);
	+	}
	+
	+	module RotorWithHoles(){
	+	difference(){
	+	Rotor(AxleRad, AxleLength, RotorEdgeSpan, RotorDisplacement, SpokeWidth, RotorHeight,AxleInnerDepth,AxleInnerRad,ScrewHoleRad);
	+	EppieCutouts(EppieRad,30);
	+	EppieCutouts(EppieRad,90);
	+	EppieCutouts(EppieRad,150);
	+	}
	+	}
	+	difference() {
	+	union() {
	+	RotorWithHoles();
	+	translate([0,0,0]) cylinder(h=5, r=23, center=yes);
	+	}
	+	translate([0,0,3.5]) cylinder(h=30, r=17, center=yes);
	+	translate([0,0,-1]) cylinder(h=30, r=12.5, center=yes);
	+	}
	+
	+	</code>

project:biolab:centrifuge-sketch

Anonymous (anonymous@undisclosed.example.com) — 2014-10-11T15:01:55+00:00

1336783513	current
Line 1:	Line 1:
	+	Centrifuge controlled over serial USB:

	+	<code lang="C">
	+	#include <Servo.h>
	+
	+	Servo disk;
	+
	+	int diskpin = 3;
	+	int diskstop = 50, diskmin = 100, diskmax = 165;
	+
	+	int optpin = 8;
	+
	+	void setup()
	+	{
	+	Serial.begin(9600);
	+	pinMode(optpin, INPUT);
	+	digitalWrite(optpin, HIGH);
	+
	+	disk.attach(diskpin);
	+	delay(2000);
	+	disk.write(diskstop);
	+	delay(3000);
	+	}
	+
	+	int cur_time = 0;
	+	int edge_ones = 0;
	+	char last_opt = 0;
	+
	+	void loop()
	+	{
	+	char optstatus = digitalRead(optpin);
	+	if (optstatus == 1 && last_opt == 0)
	+	edge_ones++;
	+	last_opt = optstatus;
	+
	+	int new_time = millis()/1000;
	+	if (new_time != cur_time) {
	+	cur_time = new_time;
	+	Serial.print(edge_ones * 60, DEC);
	+	Serial.print(" RPM ");
	+	edge_ones = 0;
	+
	+	Serial.println(optstatus, DEC);
	+
	+	if (Serial.available()) {
	+	char buf[8] = "";
	+	Serial.readBytesUntil('\n', buf, sizeof(buf));
	+	if (buf[0]) {
	+	int num = atoi(buf);
	+	Serial.println(num, DEC);
	+	if (num == 0)
	+	disk.write(diskstop);
	+	else if (1 <= num && num <= 100)
	+	disk.write(map(num, 1, 100, diskmin, diskmax));
	+	}
	+	}
	+	}
	+	}
	+	</code>
	+
	+	Centrifuge controlled via button:
	+
	+	<code lang="C">
	+	#include <Servo.h>
	+
	+	Servo disk;
	+
	+	int diskpin = 8;
	+	int diskstop = 50, diskmin = 100, diskmax = 165;
	+
	+	int optpin = 3;
	+	int btnpin = 12;
	+	int ledpin0 = 13, ledpin1 = 11;
	+
	+	void setup()
	+	{
	+	Serial.begin(9600);
	+	pinMode(optpin, INPUT);
	+	digitalWrite(optpin, HIGH);
	+
	+	pinMode(btnpin, INPUT);
	+	digitalWrite(btnpin, HIGH);
	+
	+	pinMode(ledpin0, OUTPUT);
	+	digitalWrite(ledpin0, HIGH);
	+	pinMode(ledpin1, OUTPUT);
	+	digitalWrite(ledpin1, HIGH);
	+
	+	#if 0
	+	disk.attach(diskpin);
	+	delay(2000);
	+	disk.write(diskstop);
	+	delay(3000);
	+	#else
	+	disk.attach(diskpin);
	+	disk.write(diskstop);
	+	delay(4000);
	+	#endif
	+
	+	digitalWrite(ledpin0, LOW);
	+	digitalWrite(ledpin1, LOW);
	+	}
	+
	+	int cur_time = 0;
	+	int edge_ones = 0;
	+	char last_opt = 0;
	+	int status = 0; // 0: off, 1: on
	+
	+	void loop()
	+	{
	+	char optstatus = digitalRead(optpin);
	+	if (optstatus == 1 && last_opt == 0)
	+	edge_ones++;
	+	last_opt = optstatus;
	+
	+	int new_time = millis()/1000;
	+	if (new_time != cur_time) {
	+	cur_time = new_time;
	+	Serial.print(edge_ones * 60, DEC);
	+	Serial.print(" RPM ");
	+	edge_ones = 0;
	+
	+	Serial.println(optstatus, DEC);
	+	}
	+
	+	char btnstatus = ! digitalRead(btnpin); // button press grounds the pin
	+	if (status == 0 && btnstatus == 1) {
	+	digitalWrite(ledpin0, HIGH);
	+	digitalWrite(ledpin1, HIGH);
	+	disk.write(diskmax);
	+	status = 1;
	+	} else if (status == 1 && btnstatus == 0) {
	+	disk.write(diskstop);
	+	digitalWrite(ledpin0, LOW);
	+	digitalWrite(ledpin1, LOW);
	+	status = 0;
	+	}
	+	}
	+	</code>

Incubator

Anonymous (anonymous@undisclosed.example.com) — 2016-11-25T09:47:14+00:00

1478797752		current
Line 23:		Line 23:

	**		**
-	If you are interested to partake in this project, have ideas for how to proceed, or want to donate material, contact anoone interested in [[project:biolab]]! Any help appreciated.**	+	If you are interested to partake in this project, have ideas for how to proceed, or want to donate material, contact anoone interested in [[project:biolab:start]]! Any help appreciated.**

PCR

Anonymous (anonymous@undisclosed.example.com) — 2025-06-15T08:06:37+00:00

1749973994		current
Line 5:		Line 5:
	Since 2025, we have restarted our legendary efforts to have reproducible PCR results. Running workflow includes flowbox, sterile equipment, new centrifuges and thermocyclers... and of course university-grade knowledge.		Since 2025, we have restarted our legendary efforts to have reproducible PCR results. Running workflow includes flowbox, sterile equipment, new centrifuges and thermocyclers... and of course university-grade knowledge.

-	TODO Vic textu	+	==== Bio-Rad iCycler image conventer ====
		+
		+	The iCycler software is storing images of 96-wells fluorescence activities in their own binary blob .ISI without the possibility to export to any standard format like TIFF or DICOM. So one have to hexdump and write their own conventer...
		+
		+	<code c isi2tiff.c>
		+	// Convert BIO-RAD ISI to TIFF
		+	// 16bit grayscale little-endian
		+	// CC-BY-NC sachy@brmlab
		+
		+	#include <stdio.h>
		+	#include <stdlib.h>
		+	#include <string.h>
		+	#define ISIWIDTH 342
		+	#define TIFFWIDTH 310
		+	#define TIFFHEIGHT 240
		+	#define TIFFHEAD {0x49,0x49,0x2a,0x00,0x88,0x8a,0x04,0x00}
		+
		+	unsigned char tt[]={0x11,0x00,0x00,0x01,0x03,0x00,0x01,0x00,
		+	0x00,0x00,0x36,0x01,0x00,0x00,0x01,0x01,0x03,0x00,0x01,0x00,0x00,0x00,0xf0,0x00,
		+	0x00,0x00,0x02,0x01,0x03,0x00,0x02,0x00,0x00,0x00,0x10,0x00,0x10,0x00,0x03,0x01,
		+	0x03,0x00,0x01,0x00,0x00,0x00,0x01,0x00,0x00,0x00,0x06,0x01,0x03,0x00,0x01,0x00,
		+	0x00,0x00,0x01,0x00,0x00,0x00,0x11,0x01,0x04,0x00,0x02,0x00,0x00,0x00,0x72,0x8b,
		+	0x04,0x00,0x12,0x01,0x03,0x00,0x01,0x00,0x00,0x00,0x01,0x00,0x00,0x00,0x15,0x01,
		+	0x03,0x00,0x01,0x00,0x00,0x00,0x02,0x00,0x00,0x00,0x16,0x01,0x03,0x00,0x01,0x00,
		+	0x00,0x00,0x80,0x00,0x00,0x00,0x17,0x01,0x04,0x00,0x02,0x00,0x00,0x00,0x6a,0x8b,
		+	0x04,0x00,0x1a,0x01,0x05,0x00,0x01,0x00,0x00,0x00,0x5a,0x8b,0x04,0x00,0x1b,0x01,
		+	0x05,0x00,0x01,0x00,0x00,0x00,0x62,0x8b,0x04,0x00,0x1c,0x01,0x03,0x00,0x01,0x00,
		+	0x00,0x00,0x01,0x00,0x00,0x00,0x1d,0x01,0x02,0x00,0x02,0x00,0x00,0x00,0x2d,0x00,
		+	0x00,0x00,0x28,0x01,0x03,0x00,0x01,0x00,0x00,0x00,0x02,0x00,0x00,0x00,0x52,0x01,
		+	0x03,0x00,0x01,0x00,0x00,0x00,0x01,0x00,0x00,0x00,0x53,0x01,0x03,0x00,0x02,0x00,
		+	0x00,0x00,0x01,0x00,0x01,0x00,0x00,0x00,0x00,0x00,0x48,0x00,0x00,0x00,0x01,0x00,
		+	0x00,0x00,0x48,0x00,0x00,0x00,0x01,0x00,0x00,0x00,0x00,0x6c,0x02,0x00,0x80,0x1e,
		+	0x02,0x00,0x08,0x00,0x00,0x00,0x08,0x6c,0x02,0x00};
		+
		+	int main(int argc,char argv)**
		+	{
		+	*FILE in=NULL;**
		+	*FILE out=NULL;**
		+	switch(argc)
		+	{
		+	case 2:
		+	{
		+	in=fopen(argv[1],"r");
		+	out=stdout;
		+	break;
		+	}
		+	case 3:
		+	{
		+	in=fopen(argv[1],"r");
		+	out=fopen(argv[2],"w");
		+	break;
		+	}
		+	default:
		+	case 0:
		+	case 1:
		+	{
		+	printf("isi2tif infile [outfile]");
		+	return -1;
		+	break;
		+	}
		+	}
		+
		+	*unsigned char buff[ISIWIDTH2];**
		+	*unsigned char buff2[ISIWIDTH22];*
		+	unsigned char th[]=TIFFHEAD;
		+	unsigned short h=0;
		+	*memset(buff,0x00,ISIWIDTH2);**
		+	*fread(buff,1,382,in);**
		+
		+	fwrite(th,1,sizeof(th),out);
		+	while(fread(buff,2,ISIWIDTH,in)==ISIWIDTH && h++<TIFFHEIGHT)
		+	{
		+	memset(buff2,0xFF,sizeof(buff2));
		+	for(int i=0;i<sizeof(buff)/2;i++)
		+	*memcpy(buff2+i4,buff+i2,2);*
		+
		+	*fwrite(buff2,22,TIFFWIDTH,out);**
		+	}
		+	fwrite(tt,1,sizeof(tt),out);
		+
		+	fclose(in);
		+	fclose(out);
		+	return 0;
		+	}
		+	</code>
		+
		+
		+	FIXME TODO Vic textu

Rodent Enrichment - Sketch

Anonymous (anonymous@undisclosed.example.com) — 2011-06-17T13:07:38+00:00

	current
Line 1:	Line 1:
	+	===== Rodent Enrichment - Sketch =====

	+	<code>
	+	#include <Servo.h>
	+
	+	int door_pin = 2;
	+	int sensor_pin[] = { 3, 4, 5, 6, 7, 8 };
	+	#define sensors (sizeof(sensor_pin)/sizeof(servo_pin[0]))
	+	int servo_pin[] = { 9, 10 };
	+	#define servos (sizeof(servo_pin)/sizeof(servo_pin[0]))
	+	int servo_pos[][4] = { { 80, 10, 25, 45 }, { 5, 80, 65, 45 } };
	+
	+	Servo servo[2];
	+
	+	void setup()
	+	{
	+	Serial.begin(9600);
	+	int i;
	+	pinMode(door_pin, OUTPUT);
	+	digitalWrite(door_pin, LOW);
	+	for (i = 0; i < sensors; i++)
	+	pinMode(sensor_pin[i], INPUT);
	+	for (i = 0; i < servos; i++) {
	+	servo[i].attach(servo_pin[i]);
	+	servo[i].write(servo_pos[i][2]);
	+	}
	+	}
	+
	+	void calibrate()
	+	{
	+	int i;
	+	for (i = 0; i < 80; i++) {
	+	servo[0].write(i);
	+	Serial.println(i);
	+	delay(250);
	+	}
	+	delay(1000);
	+	}
	+
	+	void sensor_info()
	+	{
	+	int i;
	+	for (i = 0; i < sensors; i++) {
	+	bool state = digitalRead(sensor_pin[i]);
	+	Serial.print(state);
	+	}
	+	Serial.println();
	+	}
	+
	+	void loop_ro()
	+	{
	+	sensor_info();
	+	digitalWrite(door_pin, LOW);
	+	delay(1000);
	+	sensor_info();
	+	digitalWrite(door_pin, HIGH);
	+	delay(1000);
	+	}
	+
	+	void loop_rw()
	+	{
	+	if (Serial.available()) {
	+	unsigned char cmd = Serial.read();
	+	int sid = 0;
	+	switch (cmd) {
	+	case 'd': digitalWrite(door_pin, LOW); break;
	+	case 'D': digitalWrite(door_pin, HIGH); break;
	+	case 'S': sid = 1; // fall through
	+	case 's': /* sid = 0; */ {
	+	unsigned char pos = Serial.read();
	+	servo[sid].write(servo_pos[sid][pos - '0']);
	+	}
	+	}
	+	}
	+	sensor_info();
	+	delay(100);
	+	}
	+
	+	void loop()
	+	{
	+	loop_rw(); return; // Interactive
	+	loop_ro(); return; // Non-interactive, door cycling
	+	calibrate(); return; // Calibrate
	+	}
	+	</code>

Project Biolab

Anonymous (anonymous@undisclosed.example.com) — 2025-09-01T14:04:54+00:00

1756735465		current
Line 14:		Line 14:
	name: Project Biolab		name: Project Biolab
	status: active		status: active
-	image: {{:project:10076716473_fb5380cf36.jpg}}	+	image: {{:project:dna.jpg}}
	----		----

Elektrostimulace chutoveho senzorickeho aparatu

Anonymous (anonymous@undisclosed.example.com) — 2019-09-20T18:36:58+00:00

1368661073		current
Line 1:		Line 1:
	===== Elektrostimulace chutoveho senzorickeho aparatu =====		===== Elektrostimulace chutoveho senzorickeho aparatu =====
		+	{{template>project:infobox\|
		+	name=Elektrostimulae\|
		+	image=dna.jpg\|
		+	founder=[[user:chido]]\|
		+	interested=TODO
		+	}}
		+
		+	~~META:
		+	status = done!
		+	&relation firstimage = :project:10076716473_fb5380cf36.jpg
		+	~~
		+

	Experimenty s elektrostimulaci ruznych oblasti jazyka nekovovymi elektrodami		Experimenty s elektrostimulaci ruznych oblasti jazyka nekovovymi elektrodami