for more News/Topics/and Meanderings
2/17/11
GenoBlasts 2011 - the ReBoot
Welcome to Year two.
This
January, I was able to meet Drew Endy, Neal Stephenson, Bruce Sterling,
Jim Thomas, Laura Dress, Amy Guttman, as well as Dr. Michaels of the
Presidential Commission for the study of Bioethical Issues all in a
period of less then 48 hours last month.
Here Be Dragons: Governing a Technologically Uncertain Future
http://newamerica.net/events/2011/here_be_dragons
http://app.mx3.americanprogressaction.org/e/es.aspx?s=785&e=178105&elq=5529f3c7212041ac9de1a5969a1ac6cb
While attending, I also had the opportunity to catch up with our friend Andrew Hessell from the Singularity University and got the delightful news that he'll be visiting the BioMore region for the near future. He has begun speaking with residents of the Node to develop communal wetlab space in the city.
Laura has offered to advise our community in matters of policy development in the region, and mentioned having access to a number of resources to help further develop synthetic biology community science.
Miles has suggested that the equipment workshop might be able to be set-up by April, so we can construct our gel boxes and PCR. Additional DIY instrument kits under consideration are Heating Baths/Shakers, Magnetic Stirrer Hotplates, PC Chassis/incubators and LED UV/Vis Spectrophotometers. This leaves purchase of freezers, refridgerators and autoclaves for any space that wants to begin playing with BSL-0 recombinant experiments.
I'd like to see if we could create a bioliteracy celebration day in tandem w JCVI and UMBI to celebrate Synthia's first year. Reaching out to educators, local industry, and policy makers.
Another idea for a class in tandem with the Baltimore Aquarium and Institute of Fluorescence would be an investigation of native ecosystem's flourescing wildlife, as well as care and cultivation.. such as foxfire or our Chesapeake Bay jellies. Personally I'd love to have a couple small terrarium/aquariums full of naturally flourescing proteins and their organisms.
Nova and Nova Science Now, have had a lot of interesting programs lately, definitely worth tracking on your DVR'S. Recently they covered BioPrinters, FOX-O the longevity gene, Artificial Photosynthesis and biofuels.
Although we haven't had much participation from the JHU students direct, I found a great little competition for our younger community members that is still registering until the end of February.
"JHU’s CISST Robo-Challenge
Websites: http://www.cisst.org/K-12-programs & http://cissrs.lcsr.jhu.edu/JHRC2010
Ages: Middle & High School
Registration Dates: January - February
Format: Individuals or Teams
Cost: ~$50 / team + cost of Robot (~$150-$500)
This is a Baltimore, Maryland based event. The JHU Robo-Challenge is a day long competition consisting of five individual robotics challenges, speakers on robotics, tours of the Hopkins campus and the robotics buildings, and lots of prizes! BoE-bot (Board of Education) robotics kit are used for this competition. The Robo-Challenge is a robot competition for high school and middle school students. There are five competitions - Petite Slalom, Mystery Course, Innovative Use of BOE kits, Tumor Detection and Robot Dance. Students will build the robot before the competition and on the day of the competition students will need to be able to program them based on the obstacle course that day. The general layout of the course will be given to students before hand, but the actual path will be unknown, and may change. This event is brought to you by Computer-Integrated Surgery Student Research Society (CISSRS) - Johns Hopkins University Laboratory for Computational Sensing and Robotics (LCSR) - Johns Hopkins University Johns Hopkins University Alumni Association."
GenoBlasts: The Reboot
January 2011
Alot has been accomplished during our first year here. We've sent a team to iGEM, coordinated with policymakers regarding issues of citizen science and synthetic biology, we've crafted hobbyist kits for gel-electro phoereAsis and pcr reactions, and built a biobrick compliant taq polymerase using single-point mutation. We've been filmed by German documentary film makers, visited by journalists and courted by reality show producers. We've founded partnerships between academia and hackerspaces, roboticists and biologists. We've met some of the founding members of DIY-Bio, as well as some of the more vocal advocates for Synthetic Biology such as Rob Carlson, and Andrew Hess/ell.
With all that, there is so much more to accomplish, and now is the perfect time to start working on the future.
Tomorrow I head to DC for two events --
Here Be Dragons: Governing a Technologically Uncertain Future
http://newamerica.net/events/2011/here_be_dragons
Synthetic Biology: The President's Bioethics Commission
http://app.mx3.americanprogressaction.org/e/es.aspx?s=785&e=178105&elq=5529f3c7212041ac9de1a5969a1ac6cb
Hope to meet my icons Neal Stephenson and Drew Endy. If you make it let's hook up.
There's a new iGEM team forming at Towson University on saturday. I believe that Dr. Burkett may also continue the CCBC team as well, bringing Maryland's iGEM contingent to 3 teams if we include JHU.
WooHoo!
I was able to meet Drew Endy, Neal Stephenson, Bruce Sterling, Jim Thomas, Laura Dress, Amy Guttman, as well as Dr. Michaels of the Presidential Commission for the study of Bioethical Issues all in a period of less then 48 hours last month. While attending, I also had the opportunity to catch up with our friend Andrew Hessell from the Singularity University and got the delightful news that he'll be visiting the BioMore region for the near future. He has begun speaking with residents of the Node to develop communal wetlab space in the city.
Laura has offered to advise our community in matters of policy development in the region, and mentioned having access to a number of resources to help further develop synthetic biology community science.
Miles has suggested that the equipment workshop might be able to be set-up by April, so we can construct our gel boxes and PCR. Additional DIY instrument kits under consideration are Heating Baths/Shakers, Magnetic Stirrer Hotplates, PC Chassis/incubators and LED UV/Vis Spectrophotometers. This leaves purchase of freezers, refridgerators and autoclaves for any space that wants to begin playing with BSL-0 recombinant experiments.
I'd like to see if we could create a bioliteracy celebration day in tandem w JCVI and UMBI to celebrate Synthia's first year. Reaching out to educators, local industry, and policy makers.
Another idea for a class in tandem with the Baltimore Aquarium and Institute of Fluorescence would be an investigation of native ecosystem's flourescing wildlife, as well as care and cultivation.. such as foxfire or our Chesapeake Bay jellies. Personally I'd love to have a couple small terrarium/aquariums full of naturally flourescing proteins and their organisms.
Nova and Nova Science Now, have had a lot of interesting programs lately, definitely worth tracking on your DVR'S. Recently they covered BioPrinters, FOX-O the longevity gene, Artificial Photosynthesis and biofuels.
Although we haven't had much participation from the JHU students direct, I found a great little competition for our younger community members that is still registering until the end of February.
"JHU’s CISST Robo-Challenge
Websites: http://www.cisst.org/K-12-programs & http://cissrs.lcsr.jhu.edu/JHRC2010
Ages: Middle & High School
Registration Dates: January - February
Format: Individuals or Teams
Cost: ~$50 / team + cost of Robot (~$150-$500)
This is a Baltimore, Maryland based event. The JHU Robo-Challenge is a day long competition consisting of five individual robotics challenges, speakers on robotics, tours of the Hopkins campus and the robotics buildings, and lots of prizes! BoE-bot (Board of Education) robotics kit are used for this competition. The Robo-Challenge is a robot competition for high school and middle school students. There are five competitions - Petite Slalom, Mystery Course, Innovative Use of BOE kits, Tumor Detection and Robot Dance. Students will build the robot before the competition and on the day of the competition students will need to be able to program them based on the obstacle course that day. The general layout of the course will be given to students before hand, but the actual path will be unknown, and may change. This event is brought to you by Computer-Integrated Surgery Student Research Society (CISSRS) - Johns Hopkins University Laboratory for Computational Sensing and Robotics (LCSR) - Johns Hopkins University Johns Hopkins University Alumni Association."
People building community, building machines, building instruments, building genes, building proteins, building connections, building understanding, building literacy, building the future, together.
- GenoBlasts: Self-Assembling since February 2010
BioMore Update 7.1.1

Above is the current revision under consideration for the iGEM Competitors.
Love to hear some feedback. Still want to do something to stylize the face. I thought about a Cyclon, suggesting the involvement of robots in our constructive apparati, and just noticed the white needing to be removed in the iGEM logo. I thought it gave it kind of a garage influence with the welder clip-art. I think we have to add some sponsor logos's as well. Hint..! (Contact Dr. Tom Burkett, if you're interested.) We've cleared our hotel and registration fees and are still working on our travel expenses as of this week.
This past monday evening, several of the team members got together to send off our project abstract by the deadline. We had to focus on what areas we were making progress in and provide a coherent vision of what we have achieved this summer since the founding of the team.
Synthetic biology research requires more cost effective approaches toward reagents and hardware accessibility. We are developing low-cost alternatives to existing hardware and enzymes in an attempt to expand participation in biological research and development.
Our project expands the accessibility of Taq Polymerase by engineering it in a form compatible with BioBrick assembly. This allows use of the over-expressed enzyme from a crude bacterial extract in a PCR reaction at a fraction of the cost of highly purified commercial enzyme. In addition, we have developed inexpensive and easily assembled lab equipment such as a gel electrophoresis apparatus and a PCR thermal cycler.
Enabling researchers to synthesize their own enzymes and having access to inexpensive tools will allow for increased participation among the DIY-bio community, stretch increasingly scarce educational funds, and allow rapid scale up of large scale gene synthesis projects."
Other Updates
DIYFest
is at the end of October and we are considering hosting a tabled
discussion on the Benefits and Concerns of Open Science approaches in
the field of biotechnology, bio-security and bio-defense for the other
DIY participants in the Baltimore region.
Miles has mostly completed both the Gel Electrophoresis and PCR plans and is in the process of creating documentation. We hope to set-up a workshop in the winter with interested individuals and local high-school biology instructors to build the kits on one day and then runs some experiments the next.
Several members of Team Baltimore had the opportunity to meet up with the founder's of DIY-Bio along with members of the New York and BioCurious folks from Berkeley in late July. It was nice to hear first hand where folks were in their interactions with their local environments, and the challenges they faced in gaining space to work, acquiring reagents, or making sense of the protocols when having varied levels of mentorship
We
are blessed to have the support and guidance of Tom, Lisa and Liz.
Thanks again for your time and experience to draw upon. I'm hoping that
we can continue to branch out and share the institutional resources
necessary to grow a skilled conscientious culture of scientific inquiry.
To begin we suggest all of our participants to take the following training on BioSafety from the CDC's Site.
Bio-Curious' head Tito, was institutional in August with hosting the Open Science Summit. Check out the video's from it here.
http://fora.tv/partner/Open_Science_Summit
The 2nd public session on BioEthics took place last week as well. Check out the videos here.
Miles was able to make it to day two, where the founder's of iGEM and
DIY-Bio were questioned about what they were up to and where the
technologies were currently at.
BioMore Update 8.1.10
We kick off August's look at BioSecurtiy, BioSafety and BioEthics with a new section in the links
that highlight self-training programs, as well as various Federal guidelines for safe research.
Check them out to prepare yourself for performing research and getting used to thinking about
various what if scenario's or "Sanity Checks!" regarding Dual Purpose research.
Great tools and they're free, Let the Training Begin.
BioMore 4.3 Wrap-Up
After a roughly a week's break from official activities the team met to discuss strategies and tactics.
A few hands have been taking up the lab tech training from Tom and Duke throughout the lazy summer days, while doing so they revisited the basic procedural steps of ligation, gel-phoresis, transformation, as well as the tasks of mixing and pouring media, basic chemical preparation, as well as safety and hygeine in the lab. Tom has also been introducing us to the concepts behind workflow and how to divide and stage the various processes towards a greater project concept.
Miles suggested that he will be working towards several ideas in hardware project construction from a PCR unit to a DNA sequencer. We discussed in depth, Patrick's idea for the creation of a cellular automaton. He broke down the previous tactics in DNA computing where everything is synthesized then re-sequenced for the answer, then posited the creation of an Artificial Neural Network type approach in utilizing various signaling proteins to reach consensus and establishing some way to create back propagation of error.
We've decided to restrict lab nights to Monday and Tuesday from 7-10pm, with a floater strategy meeting on Thursday nights so we can stimulate thought with a change of environment. With that in mind we are back tonight and look forward to seeing those of you who can make it in to keep cranking on our technique.
Ryan
BioMore 4.2 Meeting Wrap-up 6/11/10
Help me fill out our wiki... If you're on the team then log-in and help us add some information of value. Feel free to grab information from here and the blog and link-in items of value. We also need to make our graphics for the current experiment. Check Openwetware for lab notebooks and other resources. I needed to grab a new screen for my workstation, but once I get that taken care of I should be able to install maya and start playing with the tutorials to add more graphics and see what that molecular package is about. We're waiting on Tom to send in the MatLab application. Apparently they need it signed faxed and e-mailed before we can begin.
On Monday we restricted and ligated, on Tuesday we transformed and plated, on Wednesday we scratched our heads and troubleshot, on Thursday we calculated base-pairs and determined the possible source of our problem. Duke put together a Gel-Phoresis to find that we had an inadequate amount of DNA (Plasmids) to begin with. Tom had put in an order for the proper primers that work with biobrick parts and will be adding additional DNA to the order as well.
As we arrange trial#2, we should integrate the lab notebook and document the process with the tools that we've got available. Drawn out diagrams should be translated into jpegs. Protocols should be typed, with hyperlinks to the actual parts in the registry.
Colin has offered use of his digital camera and several other folks have chimed in saying they'd be happy to help document, script and help shine some illumination on these 5 or so basic techniques that are necessary to achieve viable transformations.
Besides these skills, the next important focus would be fleshing out a specific project. We've had a couple things proposed, the trick will be to identify those that are achievable within the time-frame of late august. The ability to navigate the registry with familiarity, perform database research with BLAST regarding gene sequences of interest, as well as utilizing the proper environment for the chassis of interest are key in a succesful approach. So if you have heard something amongst the various projects we've tossed around that really moves you, start poking through those tools to see what you might be able to brew up, what's already made and see if any other folks are working on something similar.
Week 2
Lab hours: Mon - Wed 7-10, Strategy meeting Thu 8-10.
Some folks have discussed coming in on some additional hours with Duke or the lab techs.
See you soon,
Ryan
BioMore 4.1 Meeting Wrap-up
June 4th 2010
Good
evening BioMore!
What a pleasant surprise tonight was, even if a bit loud and disorderly at times. There was definite progress made while herding the cats that are our various schedules.
Tom presented his experiment and answered questions about the process and goal.
To get used to dealing with the BioBrick components he had presented several articles reviewing the the quorum sensing apparatus of LuxR and LuxI, as used in Vibrio Fischeri, then showed a suggested experiment in a bacterial sensor array.
We then looked at finding parts in the registry and how the parts in our particular distribution can be found.
Remember to click on the DNA helix icon on the Registry Parts and it will give you the option of choosing a particular distribution. Unfortunately the registry isn't directly cross-referenced so you'll have to look up components separtly and then check if they're in the distribution separately or just read through the descriptions searching the html for specifics unless you have the BB part number.
We also set-up tentative lab scheduling with Duke that may morph as the calendar gets set-up and integrated by Andrew.
At this point there will be 3 main groupings of 4 to 5 folks meeting once a week from 7-10 on either Mon, Tues, Weds.
We will
also be meeting on Thursdays from 8-10 regardless of which group you're
in (if you can make it), and we will meet outside the lab on every other
sunday starting on the 13th for a few hours to collaborate, meditate,
and celebrate. Looks great, and if you can make more evenings that's
okay. But we've got one helluva a team of about 16-18 intriguing
characters.
The special on Science channel was repeating when I got home so I was able to record it, but got the discussion panel first, then it repeated the documentary. Such an exciting time to be involved in this, the hype meter in my head went ballistic. And I got a return call from JCVI tonight, but we're playing tag. My hope is to still get a speaker from them, but with their current media blitz, it may be difficult.
Start thinking about your project ideas as well, and how we might flush them out. We are currently about t-4 weeks to have an official selection.
Anyhow I'll forward the scheduling information, when I get it from Duke. Melissa, I put you in the monday evening group tenatively since you cleared your schedule for that evening, let me know if you need a change.
Clear up any last minute registration issues you may have and you can get your iGEM pin from Tom along with access to the wiki. Andy says he'll iron out our networked spaghetti web, and open up some more space on his servers for files, etc..
Take Care and See you soon,
Ryan
6/1/10 Update from Tom
- HW for this weeks meeting on the 4th.
Tom has uploaded several files to the Biomore Google group. E-mail me for access if you have not received an invite yet.
He has put together some research on quorum sensing for us to look into before this weeks meeting on thursday evening at 8pm.
Make sure to set your DVR's for the Science station if you get it, as they will be having an hour long special at 8pm Thursday on Synthetic Biology in response to the latest buzz at JCVI regarding their successful chromosomal replication experiments that have been around the media of late.
-From Tom
"Hi everyone,
A reminder that we have a meeting this coming Thursday evening starting at 8 in D-206 at CCBC. There are some people missing from this group so please pass the word along.
As promised I set up a little starter project for us to get our hands dirty with (figuratively speaking of course) and I posted some light background reading that you may be interested in. The paper on bacterial sensors is probably the most important. Pages 206, and 216-218 will get you familiar with our project which is to build a pattern forming synthetic gene network. The original paper describing the network is also posted along with a review of quorum sensing for those interested. Neither of the later are essential for understanding what we will be doing.
Also if you get a chance go to the main page of the registry of standard parts and click on the DNA repository page. Then click on the Spring 2010 distribution-this will take you to three icons depicting each of the three plates of biobrick parts. You can click on an icon and then browse through the parts included on that plate. You can also search using the part numbers-go back to the main page of the registry and click on search parts-type in the part number and you should be taken to the main page for that part.
If you have the time look up the following parts:
J23039
F2620
I13507
I731014
R0010
I0462
R0063
P0412
J04450
R0062
We'll discuss these parts and what they do on Thursday.
I should have DNA ready for us to cut and paste on Thursday night - but we might want to wait as it will take an hour to cut the DNA and another to paste - which would make a late night.
I'll post this to Ryan's e-mail list in case I missed anyone.
Tom Burkett, Ph.D.
Director, Biotechnology and Biomanufacturing
The Community College of Baltimore County
800 South Rolling Road
Catonsville, MD 21228
443-840-4842
tburkett@ccbcmd.edu"
iGEM Course Cost Breakdown
5/25/10 BioMore 3.4 Meeting wrap-up
Last nights meeting meandered a little.
Tom discussed the iGEM conference that he and Andy attended this past weekend in
Urbana. Among the highlights he reported were considerations on fund raising,
proper characterizations, building on previous projects that have been
attempted, and comparison of our equipment with that needed/used by other
institutions.
Fund Raising - According to the budgets quoted to Tom at iGEM the minimum range
to stay competitive fell at around $20,000 - 60,000. This means we've got to
have the mentors thinking about who might benefit from aligning themselves with
our project, and getting a hold of them right away. Employers in the industry,
technology councils, equipment manufacturers, who are the folks who might be
interested in seeing progress? With JCVI on NPR this week there is a new found
interest in the topic and it's hot in the press. This is a perfect time to
approach sponsors.
Characterizations and building on previous work - It is imperative that people
start reading the papers that Tom has posted on the BioMore group and begin to
play around with the Registry of Standard Parts to see what's available and how
it works. While doing so, the varying levels of documentation available will
become apparent and you will understand why the organizers would like some
scientific secretarialism coming behind previous projects and verifying /
documenting efficacy.
Patrick expanded upon the automaton model suggested last meeting and we began to
discuss the nature of microbial colonies and their ability to send/receive
various signals. I suggested that folks check out the video "Tiny Conspiracies"
[http://www.clicker.com/web/microbeworld-video/Tiny-Conspiracies-332035.html]
put out by Microbeworld on this very topic of microbial communication. It gives
some nice insight into the various mechanisms and signalling complexes contained
within these lil workers.
I'll be heading over to the Department of Natural Resources to follow up on my
questioning on top local environmental concerns that we may be able to address
later this week.
Tom is having Scott Forester and Liz over to the lab on Friday afternoon, and if
you'd like to join him, drop him an e-mail.
tburkett@ccbcmd.edu
Next meeting will be held on Thursday evening, June 3rd, 2010 at 8 pm in Rm D206
of CCBC - Catonsville. We will be looking to nail down availability for lab
hours at that meeting, as several of you who have registered were not available
last night for comment. Tom is arranging a few simple projects for us to
assemble in the lab to give us more hands on experience with the techniques and
tools. The class officially begins next wednesday the 2nd. We need you to
register ASAP, and notify Tom with any issues you encounter so he can help to
clear them up. Several folks have suggested that they have had issues with the
registration, if this applies to you, please follow up with Tom and let him
know.
It was nice to see you again. Let's get to work...!
Ryan
5/17/10
Things went well on Monday night.
We began by looking at the transformations performed at the lab orientation on saturday reviewing the process and seeing where things may have gone wrong or right.
Tom then presented a power point on using the biobricks process to build a lead
detecting gene. Showing how to map out the process and divide the work into
steps that can be built in parallel then combined.
This brought up the question regarding time periods for building various steps
in regards to the time we have to finish our project. Miles suggested using
basic engineering concepts to find a way that quality control can be assured
along the way, rather than finding out that the project is hosed 6 weeks into
the process.
Other project concepts regarding computational biology, or building Turing
automatons was pitched by Patrick, as he explained what is currently being
performed in the field. This brought up the idea from Miles about discovering
the strengths of working with the biological model in comparison with the
standard electrical engineering model, so that the field of synthetic biology
can be tuned to capitalize on said strengths.
Alot of good discussion took place and we got out around 9:45 again.
We are on track to meet next on Monday May 24th at 8pm in Room D206,
CCBC-Catonsville. The official class start is in about 2 weeks and we need to
present schedule availability over the summer as Robert has previously
suggested, so we can see what hours participants will have available to work in
the lab this summer.
I'll start.. My current work schedule has me rubbing folks on Thursday to
Saturday 10-7 in Annapolis. Otherwise I'm flexible. I've been planning to be in
the lab at some point on Mon-Wed for a few hours a day, if there will be stuff
to do. I could be there for morning/afternoon/evening hours or a combination
thereof on any of those days, depending on when people want to meet. Remember we
alone are responsible for our schedule, so give it some thought in regards to
the level of commitment you can offer.
Tom and Andy are booked to head to Urbana this weekend for the spring workshop
and we hope to learn much from their journey. The biobrick has arrived and as
Duke begins to replicate parts for us, we can start using them. Of course we
only receive the 1000 most used parts, so if we come up with a project idea that
requires a part that we didn't receive we'll need to order them from iGEM asap.
Finals are behind me, so I can spend a little more time focusing on the
community, and I want to say "Thank You" to you all for being patient with me
while I learn to balance my work-flow.
Take Care,
Ryan
5/10/10
For those of you more familiar, thanks for being patient while the rest of us catch up on the curve.
So we decided tonight to meet on monday evenings in the lab at 8pm in succession until the summer session begins, during which time we'll go over basic knowledge and skills to put into practice once the brick arrives. It should have already arrived so Tom will be contacting Meagan at iGEM to see where they're at in the process.
Here is the link I received from Michelle Williams on the DIY-Bio Security piece. It's actually much better then I thought from the title.
http://burnafterreading.nationaljournal.com/2010/05/citizen-scientists-attract-fbi.php
I will post the power point on the biobrick parts as soon as I receive it from Tom.
For now the interested participants are expected to start flushing out the concept projects and their pitch to be presented in June as we refine initial ideas. Regional environmentally conscious projects regarding power generation and bio-remediation seem to be at the forefront of the ideas that were discussed so far. Although the self-assembly bridge building gaussian field sensitive microbots might be a ways down the road, I am looking forward to learning more from Liz once her schedule can make her available to us. I also will attempt to see if we can get JCVI's education outreach to lend us a speaker still.
This Saturday the 15th is the 2nd Lab Orientation from 10 am - 2 pm in Room D206 at Catonsville's CCBC. Remember that attendance in one of the lab orientations is mandatory to participate. Tom will be scheduling another at the beginning of June as well.
Once again, for those of you interested that can make it, we are meeting again next monday May 17th @ 8 pm at the lab. (Rm D206 - Catonsville CCBC)
Ryan
5/4/2010
The BioBrick had not yet arrived as of the meeting but around 6 folks made it out for the first Lab Orientation on the 1st, where they began to think about possible projects for the competition. The basic question of what can/can't be achieved/was reasonable to achieve in the short time period of the summer came up. Upon review we see that projects from software abstraction to multiple organism systems engineering are all possible, however actually getting familiar with the Registry of Standard Parts [http://www.biobricks.org/] and it's format is the most important first step. Yes, it is a foreign language for many of us still, however if you begin to check it out and ask questions, we can start getting clarity for you.
Initial ideas ranged from building self-assembly goo-bridges to
carbon-sequestration technologies, lead-sensitive bacterias, microbial
interferometers and magnetobacteria and water bioremediation amongst the Bay and the Potomac.
I think it's important to get our hands on these initial parts asap, so we can start tinkering. Our hope is that it will have arrived by next week and
hopefully we'll have the AC to go along with it. In the meantime, you can try your hand at assembling the parts with the virtual tool
http://www.genocad.orgopensource software for use with the registry.
In order to streamline communication among the team members, Robert has volunteered to create a Google Group - BioMore to facilitate intra-team messaging.
There have been quite a few resources collected amongst the pages of the BioMore GenoBlasts website at http://www.genoblasts.comand http://www.bio-more.us
As soon as you are registered Tom will forward the iGEM team wiki as well, which will have a team page posted at http://openwetware.org/wiki/IGEM.
In regards to DIY-Bio, some things that Boston has been up to are creating Microbial Fuel Cells and a digital stage for the hacked webcam microscopes they've made. Ideas in regards to the systems engineering approach of multi-microbe systems would fall very neatly into this area. A really nice video on Microbial Communications is found here..
[http://www.clicker.com/web/microbeworld-video/Tiny-Conspiracies-332035.html]
See you next week, and if you haven't attended the Lab Orientation yet make sure to clear your schedule for May 15th where we'll be meeting at the lab (Rm D206-CCBC Catonsville), between 10-2. Attendence of a Lab Orientation is mandatory for participation in the summer independent study course.
Have a great week,
Ryan
It's been a hectic month around here. I'm in the midst of a move to Annapolis,
while finishing up the last few weeks of Spring semester and time has flown
right by without alot of activity on the site here.
So here's where we stand... We have had a number of individuals show up to the
last two meetings claiming interest in both the DIY-Bio community and
participation in this year's iGEM competition. We have created an iGEM team with
a 1 credit independent study class at CCBC-Catonsville, that will allow members
of the community to come in and participate for the low cost of only $142. The
program will be structured by those who partake. In order to be on the team and
take the class you must attend one of the two Lab Orientations taking place on
May 1st and May 15th (saturdays) between 10 and 2. It suggested that interested
mentors and other members of the DIY-Bio community attend one of these events to
get idea of standard safety protocols, equipment, and methods of basic
biotechnology. Please RSVP with Dr. Tom to let him know how many people to
expect on each day. His e-mail is tburkett@ccbcmd.edu
[mailto:tburkett@ccbcmd.edu]
Michelle has forwarded me the mp3 from the meeting on the 13th. So feel free to
check it out if you were unable to make it, or want to revisit some of the ideas
that were presented.The mp3 is located here...
http://www.genoblasts.com/resources/Audio/041210_BioMoreMeeting2.0.mp3]
If you are interested in getting hands on experience then please register for
the class ASAP. You can register now, and pay by June 1st. We need to get an
idea of who will be participating, and we need to begin coming up with ideas for
projects. Some of you in the DIY community have expressed concern about
copyright, and once again in the spirit of accessibility we honor the
open-source ideals in hopes that we can educate and spread the availability of
these technologies.
We're working on getting a DNA Synthesizer from Julie Wolf at UMBC for the
WetLab space at Harford Hackerspace, and hope to hear back from her soon, as she
brought up the idea with her board of directors. Tom doesn't want older
equipment like that taking up space at his lab, but since Harford is already
established as a 501c3 they would be able to forward the paperwork for the
donation to take place.
We have yet to hear back from JCVI in regards to having one of their presenters
speak with us on Monday the 3rd of May, 8pm Rm D206 CCBC-Catonsville. We are
however expecting the BioBrick to arrive in the next few days and hope that if
it's here by Monday we can start digging into the materials and coming up with
some concrete plans. Make certain that any friends that you've told about this
that have expressed interest come out to see what's going on.
If you are interested in being a member of the community and getting involved
please join us Monday night and one of the lab orientations so we can begin
seeing results.
Here are two articles discussing characterization of BioBricks parts, to get you
thinking about what we might add to the collective WetWare...
Nature : Five Hard Truths for Synthetic Biology
[http://www.nature.com/news/2010/100120/full/463288a.html]
[http://www.nature.com/news/2010/100120/full/463288a.html]
Journal of Biological Engineering : Measuring the activity of BioBrick Promoters
using an in vivo reference standard [http://jbioleng.org/content/3/1/4/]
Last - I did finally start to get some input on the forum and blog, that's right
spam. I guess I need to update to the next security measure to screen bots. I
have only received e-mail feedback from a few of you that have attended the last
two meetings, and it helps me to maintain interest focus when I get some
interaction from the community outside myself. What do folks want to do with
these tools?
Hope to see you Monday the 3rd of May, 8pm Rm D206 CCBC-Catonsville for our
third meeting. I will be in attendance on the Lab Orientation on the 15th, but
hope that folks are able to connect with Tom to come out this saturday.
Take Care,
Ryan
3/19/10
This just in from Dr. Burkett.
“I also set up a course (BIOL 281-Cooperative Education: Biology (Section PZ1; CRN# 52644) with a special note section that it is for the iGEM competition. It is a one credit course so the financials shouldn’t be too onerous for anyone ( about $100.00 for in county). If we could work out a way that Towson students or Howard students, or UMBC students could get a credit for the course that would be great. I don’t think there will be any requirement for mentors to pay the fee. I’m going to look into some mechanism so that qualified mentors can have better access to the lab-not sure what that would be right now but I’ll work on it.”
So we’re in. We’ll be holding a second meeting 8 pm on Monday, April 12th in Rm D206: CCBC- Catonsville’s Biotechnology lab.
This will be an opportunity to differentiate DIY-Bio vs. iGEM 2010 team and how these projects will interact to feed the community of interested.
Note that DIY-Bio communities from Boston, NYC, and LA are also attempting to get their teams in. If you thought this was just for kids, it’s time to step up and represent BioMore.
Suggested Agenda items to be considered.
DIY-Bio projects (Re-imagining the design of the Sythesizer/Microarray)
iGEM competition projects and interactions
Outreach opportunities:Discussing Robotfest Table
Considerations for Lecture Series / Workshops
Employment Opportunities / Networking
If I can get a decent headcount, I’ll try and clear the supplies we’ll need to do the DNA extraction, otherwise we’ll save it for Robotfest demonstrations.
WOOHOO!
3/18/10So there is certainly signs of momentum building.
This just in from Dr. Tom Burkett, our main mentor contact and head of the biotechnology department at CCBC-Catonsville.
“I’ve got a 1 credit course set up for the summer. It’s BIOL 281-Cooperative Education -Biology. There’s a note describing the course as for the iGEM competition. The course should be open for registration next week. I’m also close to finalizing the funding for the entry fee-again I should know by early next week. If possible I want to get everything registered before spring break. I talked with the iGEM people a bit today and they had no problems with DYI-Bio participation as long as they are registered at an accredited institution.
Towson is in, and drumming up support. I think there may be more interest and participation once we have the infrastructure all set up. ”
—
Patrick also sent word of further Towson interest from Elizabeth Goode, as well as Jim Saunders, who runs the molecular bio, biochemistry and bioinformatics program at towson, and he seemed cautiously enthused in his response:
“…I told Tom that I would be glad to help out as well, although the nature of the project might require that we seek specific expertise in targeted area. Both Tom and I are in a position to offer research credit for students engaging in the competition, however, we are hopeful that we might be able to find funding sources for student stipends if we engage in this activity in the future. Please let me know what the next step would be.”
We have also had contact from Prof. Lindahl and Asst. Prof. Erill from UMBC, who are still gauging the level of interest and involvement yet seem enthused.
HCCC is out as an institutional support, however Engineering Professor, Scott Foerster still remains interested in mentoring if he can.
The timing seems to be perfect for the implantation of these seeds. Two days after announcing our exploratory meeting, I was told of an organizational meeting of the DC DIY-Bio enthusiasts. This was followed by contacting security expert Piers Millet of iGEM, who put me in contact with Agent You at the FBI in DC… He just happened to be holding a webcast devoted to these issues with Jason from DIY-Bio Boston, the next day in Washington.
I also held a video interview with reporter Michelle Williams of National Journal who is doing a piece on synbio and look forward to seeing the results of her report when it’s finished.
I was also contacted by organizers of Boston, NYC, and LA: DIY-Bio groups and they also have intentions to enter iGEM possibly with similar strategies of inter-institutional support. Due to this level of interest, I have heard rumor of iGEM creating a DIY community category.
We’ll see.
Optimistically,
-Ryan
3/18/10Professor Burkett is busy putting together the specifics of the iGEM independent credit program for this summer. The goal of which is to allow accessibility to the tools in controlled lab environments. A mentor Towson University has also expressed interest in working with us, so additional lab-space may also manifest itself there.
The robotics enthusiasts from Harford Hackerspace are also interested in creating some 501c community wetlab space, and suggested that we chair a table at this next month's Robot Competition in Linthicum. Sounds like a winning idea to me. If anyone can make it to Frederick friday, the biobeers are having their social that evening.
BioSecurity
How synthetic biology is changing
the way we look at biological threats
We'll be meeting with Agent You in the future.
Success !!
The meeting went great tonight. About 20 interested individuals showed up to find out exactly what all this iGEM talk is about. About 10 committed to take part in some way or other. And now move forth to secure our registration funding, hopefully by the 21st of March. :) The folks that attended got a chance to see 1 of the proposed lab spaces, and some of the equipment that may be involved. We discussed goals, reasons to utilize the iGEM challenge as a launching ground to found a larger communal entity for the open discussion of techniques and ideas in the world of WetWare and Synthetic Biology. We thank all of you who attended, and urge you to introduce the concept to other folks you think may be interested in participating further.I will keep you updated as more information and a schedule of events unfold. Until then make sure to check out the links and primer pages, sending me any links that you would like to include. I look forward to meeting you and thank you once more for your interest and participation.
Take Care and Control,
Ryan Ogle, LMT
admin@genoblasts.com