Education Planning Meeting
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Andre Masella
Nov 2, 2009, 10:14:08 PM11/2/09
to igemcanada
Development of educational tools seemed to be on everyone's mind at
the Jamboree. I'd like to hold a meeting to get things rolling in a
few weeks. Please RSVP/select a time using Doodle:
http://www.doodle.com/38eartccya8wuxq3
I will investigate the best conferencing option and report back later.
As for curriculum development, I think we need to consider the
following questions:
1) What do you think needs to be taught and to whom?
2) Do you have people who would be willing to prepare this material?
3) Do you have existing material we can make use of?
4) How can your university provide tools to make educational materials
(e.g., recording videos)? How much does this cost?
5) How do you think this should be licensed?
The goal of the meeting would be to agree on these points (at least in
principle) and create a path forward.
If you have any other thoughts or questions that you think need to be
answered, please post them here.
the Jamboree. I'd like to hold a meeting to get things rolling in a
few weeks. Please RSVP/select a time using Doodle:
http://www.doodle.com/38eartccya8wuxq3
I will investigate the best conferencing option and report back later.
As for curriculum development, I think we need to consider the
following questions:
1) What do you think needs to be taught and to whom?
2) Do you have people who would be willing to prepare this material?
3) Do you have existing material we can make use of?
4) How can your university provide tools to make educational materials
(e.g., recording videos)? How much does this cost?
5) How do you think this should be licensed?
The goal of the meeting would be to agree on these points (at least in
principle) and create a path forward.
If you have any other thoughts or questions that you think need to be
answered, please post them here.
gc
Nov 4, 2009, 12:31:49 PM11/4/09
to igemcanada
Several people have asked me about the synthetic biology text books I
mentioned in the talk. I have uploaded a word document wherein I have
pasted screenshots containing information about these texts. As well,
there is a 2007 paper which discusses the need for synthetic biology
curriculum. Cheers!
mentioned in the talk. I have uploaded a word document wherein I have
pasted screenshots containing information about these texts. As well,
there is a 2007 paper which discusses the need for synthetic biology
curriculum. Cheers!
Eric Ma
Nov 5, 2009, 12:46:09 AM11/5/09
to igemc...@googlegroups.com
Certainly we needn't re-invent the wheel, which is why great textbooks like the ones Graham have suggested are really important. Thanks so much for providing us with those links, Graham!
Cheers,
Eric
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That said, I think we can work together to develop a centralized resource for all iGEM teams in Canada. Briefly, while daydreaming before studying for my mid-term (this Friday), I had a vision in my head of a wiki-based system for this resource, so that it's easily updatable and accessible by everybody.
Just imagine it to be a Wikipedia of iGEM resources in Canada. Embedded videos from YouTube, community-editable information & content that is cross-referenced etc.; we could even try incorporating links to social media (like Facebook, Delicious, Twitter, Digg etc.), to get the word out. It could serve as our discussion ground for throwing out and proposing new ideas amongst the Canadian community and beyond. Since iGEM is so intensely promoting the Wiki format, it also becomes a foundation for us to practice using the wiki syntax as well prior to use of the actual iGEM wikis.
Perhaps this could be our "platform", then? What do you all think? Do we have the expertise to set this up and get it going?
Cheers,
Eric
---------------------------------------------------------------
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gc
Nov 5, 2009, 10:38:40 AM11/5/09
to igemcanada
It is worth noting that the team at Waterloo has been working on a
similar idea. Incorporating a wiki-like environment for exchange of
information *is a great idea. Of course, at the base level we need
nothing more than OpenWetWare to accomplish this. In our efforts to
design such a server ourselves we discovered that bandwidth and
scalability were significant issues - the results were less than
satisfactory in two separate attempts. In contributing to the
development of the server at OICR we gain a significant boost in our
productivity which can now be focused on the content rather than the
container. It's a scalable, responsive implementation that frees us
from having to maintain hardware, backups etc. That is not to say
that we won't implement a wiki environment, we still recognize this as
a desire feature.
I'd also like to address the concept of a "Federation of iGEM teams"
because there is a tendency, I think, for people to forget that we're
thinking bigger than iGEM here. Declaring an "iGEM Canada" or "cGEM"
or "ehGEM" fosters this misinterpretation. A federation of iGEM teams
does not need a job board, is not concerned with training beyond what
it takes to accomplish an iGEM project, is only concerned about
funding in so far as each team wants a piece of a collective pie, is
not a coherent voice of authority on synthetic biology, and doesn't
really care how synthetic biology programs and industry partners in
biotechnology will affect the economy. They just want to do iGEM
better (that's a great thing in itself). A national synthetic biology
organization which incorporates interested individuals at all levels
of participation does care about these things. That means supporting
and fostering iGEM teams *and doing a whole lot more.
<snip>
similar idea. Incorporating a wiki-like environment for exchange of
information *is a great idea. Of course, at the base level we need
nothing more than OpenWetWare to accomplish this. In our efforts to
design such a server ourselves we discovered that bandwidth and
scalability were significant issues - the results were less than
satisfactory in two separate attempts. In contributing to the
development of the server at OICR we gain a significant boost in our
productivity which can now be focused on the content rather than the
container. It's a scalable, responsive implementation that frees us
from having to maintain hardware, backups etc. That is not to say
that we won't implement a wiki environment, we still recognize this as
a desire feature.
I'd also like to address the concept of a "Federation of iGEM teams"
because there is a tendency, I think, for people to forget that we're
thinking bigger than iGEM here. Declaring an "iGEM Canada" or "cGEM"
or "ehGEM" fosters this misinterpretation. A federation of iGEM teams
does not need a job board, is not concerned with training beyond what
it takes to accomplish an iGEM project, is only concerned about
funding in so far as each team wants a piece of a collective pie, is
not a coherent voice of authority on synthetic biology, and doesn't
really care how synthetic biology programs and industry partners in
biotechnology will affect the economy. They just want to do iGEM
better (that's a great thing in itself). A national synthetic biology
organization which incorporates interested individuals at all levels
of participation does care about these things. That means supporting
and fostering iGEM teams *and doing a whole lot more.
<snip>
Eddie Yee Tak Ma
Nov 5, 2009, 4:51:01 PM11/5/09
to igemcanada
Hi,
I have been spinning a few ideas on a crash course through useful
computer assisted biology geared toward iGemmers from non-computer
science.
I feel this course can offer a prototype that we can evaluate, touch
and model other courses onto.
Current crash course is modeled as a six session course, each session
being one hour long.
Uses instructional, demonstration and task oriented learning for the
course participants.
Current curriculum focuses on:
- PERL, Python, R
- General understanding of how to script, program
- Effective use of OS features (Windows, Unix)
Will offer better discussion / description when we get to meeting.
- Ed.
I have been spinning a few ideas on a crash course through useful
computer assisted biology geared toward iGemmers from non-computer
science.
I feel this course can offer a prototype that we can evaluate, touch
and model other courses onto.
Current crash course is modeled as a six session course, each session
being one hour long.
Uses instructional, demonstration and task oriented learning for the
course participants.
Current curriculum focuses on:
- PERL, Python, R
- General understanding of how to script, program
- Effective use of OS features (Windows, Unix)
Will offer better discussion / description when we get to meeting.
- Ed.
Danielle
Nov 5, 2009, 5:16:17 PM11/5/09
to igemcanada
One of the great things to come out of Saturday's meeting was the
chance to hear from other Canadian iGEMers about what the issues most
immediately important and relevant to them are. Based both on what
ended up being the focus of discussion at the meeting, and on various
chats I had with other Canadian members during the Jamboree, it seems
like what people are wanting are the things that fit perfectly into
the role of a federation of Canadian teams.
Personally, I have the same long-term vision for a Canadian synthetic
biology community that Graham has described, particularly because of
the benefits there would be to past and present (and future) members
of our iGEM teams, and I look forward to working towards those goals.
But I think the most productive thing we as iGEMers can do right now
to drive synbio growth in Canada is to organize ourselves and help
each other succeed in the competition: the work being done by our
teams is constitutes a *major* component of the truly "synthetic
biology" research currently being done in Canada. And while some PIs
(and companies funding/performing R&D) are excited about the prospects
of synbio, there's still a general reluctance to push out into that
area, and strong performance and concrete results from iGEM teams
stand to do a lot to change that.
That aside, there are specific tasks that even a handful of us
together can start working on immediately, such as the online resource
Eric has described. Like Graham said, some of us on the Waterloo team
have been exploring implementation options for building something like
this on iGEM.ca (a test site for one possibility is already up for
viewing/playing with -- we're eager for everyone else's opinions/
contributions, but let's keep discussion of that to the website
thread). These kinds of things will directly benefit our teams in the
short term, hopefully facilitating stronger outcomes for next year's
cohort of iGEMers.
Indulging in optimism for a moment, the way I envision the
relationship between all of these things is this:
If we work together to make it easier to start and to run an iGEM
team, not only will the existing teams be more successful, but more
schools will be able to start and maintain their own teams. At
Waterloo, the enthusiasm and activities of our iGEM team has had a
tremendous influence on the views of several faculty members regarding
synbio, and as a result there's already been movement toward starting
new research in the area and even developing undergraduate and
graduate programs in synbio. And I think there are already a couple of
synbio courses at at least one of the Albertan schools (corrections?).
If we can get this happening at more schools, this would be amazing.
More strong teams means more successful iGEMers and iGEM alumni, and
in turn more people to get excited about the possibilities of synbio
and work toward building a vibrant national synthetic biology
community that won't fizzle out if a few people get too busy. And I
think this is a real possibility for even just a year or two down the
line, but I'd be cautious of casting too large a net too early, when
we haven't yet built a strong foundation beneath us.
chance to hear from other Canadian iGEMers about what the issues most
immediately important and relevant to them are. Based both on what
ended up being the focus of discussion at the meeting, and on various
chats I had with other Canadian members during the Jamboree, it seems
like what people are wanting are the things that fit perfectly into
the role of a federation of Canadian teams.
Personally, I have the same long-term vision for a Canadian synthetic
biology community that Graham has described, particularly because of
the benefits there would be to past and present (and future) members
of our iGEM teams, and I look forward to working towards those goals.
But I think the most productive thing we as iGEMers can do right now
to drive synbio growth in Canada is to organize ourselves and help
each other succeed in the competition: the work being done by our
teams is constitutes a *major* component of the truly "synthetic
biology" research currently being done in Canada. And while some PIs
(and companies funding/performing R&D) are excited about the prospects
of synbio, there's still a general reluctance to push out into that
area, and strong performance and concrete results from iGEM teams
stand to do a lot to change that.
That aside, there are specific tasks that even a handful of us
together can start working on immediately, such as the online resource
Eric has described. Like Graham said, some of us on the Waterloo team
have been exploring implementation options for building something like
this on iGEM.ca (a test site for one possibility is already up for
viewing/playing with -- we're eager for everyone else's opinions/
contributions, but let's keep discussion of that to the website
thread). These kinds of things will directly benefit our teams in the
short term, hopefully facilitating stronger outcomes for next year's
cohort of iGEMers.
Indulging in optimism for a moment, the way I envision the
relationship between all of these things is this:
If we work together to make it easier to start and to run an iGEM
team, not only will the existing teams be more successful, but more
schools will be able to start and maintain their own teams. At
Waterloo, the enthusiasm and activities of our iGEM team has had a
tremendous influence on the views of several faculty members regarding
synbio, and as a result there's already been movement toward starting
new research in the area and even developing undergraduate and
graduate programs in synbio. And I think there are already a couple of
synbio courses at at least one of the Albertan schools (corrections?).
If we can get this happening at more schools, this would be amazing.
More strong teams means more successful iGEMers and iGEM alumni, and
in turn more people to get excited about the possibilities of synbio
and work toward building a vibrant national synthetic biology
community that won't fizzle out if a few people get too busy. And I
think this is a real possibility for even just a year or two down the
line, but I'd be cautious of casting too large a net too early, when
we haven't yet built a strong foundation beneath us.
gc
Nov 5, 2009, 5:54:06 PM11/5/09
to igemcanada
I agree with Danielle and, in so far as a major proposed goal of the
national organization is to foster our iGEM teams, I think there are
many synergies to be obtained in working towards a common set of
resources and a strong sense of community.
<snip>
national organization is to foster our iGEM teams, I think there are
many synergies to be obtained in working towards a common set of
resources and a strong sense of community.
<snip>
Andre Masella
Nov 5, 2009, 7:03:04 PM11/5/09
to igemcanada
This discussion about whether iGEM Canada should or should not be an
umbrella organisation is off-topic for this thread. For the purposes
of this thread, assume iGEM Canada *only* as a “federation of iGEM
teams”. I will start a thread for this other discussion.
Also, I like a wiki in principle, but I worry about curation. I think
it is important we develop some review process to avoid collecting
cruft in the wiki.
umbrella organisation is off-topic for this thread. For the purposes
of this thread, assume iGEM Canada *only* as a “federation of iGEM
teams”. I will start a thread for this other discussion.
Also, I like a wiki in principle, but I worry about curation. I think
it is important we develop some review process to avoid collecting
cruft in the wiki.
Andre Masella
Nov 16, 2009, 7:35:56 PM11/16/09
to igemcanada
The Doodle hasn't yielded a good time slot without excluding several
people. I'd like to reschedule if that's okay. As a side problem,
Skype kind of sucks for large conferences. Eddie is investigating
alternatives, so it makes sense to wait and see. More on that as it
develops. Does anyone mind?
In other news, I want to create a Biology for Engineers course. My
basic curriculum would be:
- Enzymes as the functional units of biology
- Transcription + Translation
- Regulation at enzymatic, protein-protein interactional, genetic,
transcriptional, and translational levels
- Biological materials (macromolecules - structure & function)
- Cell metabolism (Kreb's, aminoacid/fatty-acid/cell-wall
biosynthesis, proteolysis in stationary phase, DNA replication)
- Information transfer systems (e.g., signal transduction, quorum
sensing)
- Gene transfer (conjugation, viruses, transposons) + Restriction
Enzymes
- Taxonomy, Enzyme Categories, and Naming Systems
I'm basically trying to pre-format biology for an engineer's
brain...assuming my brain is typical of an engineer's brain. I think a
bottom-up approach is what engineers are used to. I'm hoping to make
short (½h) videos. I realise that outline is vague...I'll work to
expand it further. Comments?
people. I'd like to reschedule if that's okay. As a side problem,
Skype kind of sucks for large conferences. Eddie is investigating
alternatives, so it makes sense to wait and see. More on that as it
develops. Does anyone mind?
In other news, I want to create a Biology for Engineers course. My
basic curriculum would be:
- Enzymes as the functional units of biology
- Transcription + Translation
- Regulation at enzymatic, protein-protein interactional, genetic,
transcriptional, and translational levels
- Biological materials (macromolecules - structure & function)
- Cell metabolism (Kreb's, aminoacid/fatty-acid/cell-wall
biosynthesis, proteolysis in stationary phase, DNA replication)
- Information transfer systems (e.g., signal transduction, quorum
sensing)
- Gene transfer (conjugation, viruses, transposons) + Restriction
Enzymes
- Taxonomy, Enzyme Categories, and Naming Systems
I'm basically trying to pre-format biology for an engineer's
brain...assuming my brain is typical of an engineer's brain. I think a
bottom-up approach is what engineers are used to. I'm hoping to make
short (½h) videos. I realise that outline is vague...I'll work to
expand it further. Comments?
Eric Ma
Nov 16, 2009, 7:58:37 PM11/16/09
to igemc...@googlegroups.com
The curriculum looks great, Andre. What kind of level of detail were you looking at?
Cheers,
Eric
---------------------------------------------------------------
Please consider the environment before printing this e-mail. Do you really need to print it?
Cheers,
Eric
---------------------------------------------------------------
Please consider the environment before printing this e-mail. Do you really need to print it?
Andre Masella
Nov 16, 2009, 8:27:55 PM11/16/09
to igemcanada
I'm hoping to be reasonably detailed. For translation, I'd like to get
down to the level of A and P site in the ribosome, peptide bond
formation, and such. In all cases, I'd focus more on the general
mechanism through an example, rather than trying to exhaustively cover
all known systems.
Most importantly, I'd like to cut out all the “how this was
discovered” stuff that is normally part of introductory biology. Every
introductory biology course I've seen start of by explaining what
spontaneous generation is and why it's wrong...which is a waste of
time in my opinion.
down to the level of A and P site in the ribosome, peptide bond
formation, and such. In all cases, I'd focus more on the general
mechanism through an example, rather than trying to exhaustively cover
all known systems.
Most importantly, I'd like to cut out all the “how this was
discovered” stuff that is normally part of introductory biology. Every
introductory biology course I've seen start of by explaining what
spontaneous generation is and why it's wrong...which is a waste of
time in my opinion.
gc
Nov 16, 2009, 8:57:19 PM11/16/09
to igemcanada
Re-sched suits me, kinda buried here.
That's a pretty ambitious task you've set for yourself. A possible
way forward is organizing around a workshop format with multiple
speakers to distribute the load.
<snip>
That's a pretty ambitious task you've set for yourself. A possible
way forward is organizing around a workshop format with multiple
speakers to distribute the load.
<snip>
Andre Masella
Nov 27, 2009, 9:10:38 PM11/27/09
to igemcanada
Danielle brought this to my attention: http://www.biologyforengineers.org/
There's a CD available to download. Please have a look and see if it
is worthwhile.
Also, I've been meaning to reschedule the meeting. I know that now is
a hectic time. Should I try to schedule something now-ish or wait
until later when most people's exams are finished?
There's a CD available to download. Please have a look and see if it
is worthwhile.
Also, I've been meaning to reschedule the meeting. I know that now is
a hectic time. Should I try to schedule something now-ish or wait
until later when most people's exams are finished?
Eric Ma
Nov 27, 2009, 9:14:43 PM11/27/09
to igemc...@googlegroups.com
Hey everybody,
I think that after exams would be a great time to start meeting up,
especially in consideration of my fellow peers who have exams to
tackle.
My exams end on the 15th; when do everybody else's end (for those who
are students)?
Cheers
Eric
--
I think that after exams would be a great time to start meeting up,
especially in consideration of my fellow peers who have exams to
tackle.
My exams end on the 15th; when do everybody else's end (for those who
are students)?
Cheers
Eric
Danielle Nash
Nov 27, 2009, 9:39:31 PM11/27/09
to igemc...@googlegroups.com
Hi all.
I thought the CD looked pretty good; not sure how it compares content-wise to what Andre has in mind...Andre?
I'm done on the 9th, but I'll be away from the 14th until January. If mid-late December works for most people though, I can certainly just catch up on what's going on once I return.
Danielle
I thought the CD looked pretty good; not sure how it compares content-wise to what Andre has in mind...Andre?
I'm done on the 9th, but I'll be away from the 14th until January. If mid-late December works for most people though, I can certainly just catch up on what's going on once I return.
Danielle
Message has been deleted
K.Zhan
Nov 27, 2009, 10:28:02 PM11/27/09
to igemcanada
Hey Everyone,
I have yet to look at the CD yet.
However for the meeting I think we should get it done as soon as
possible. For those of you who know me I kind of have that lets just
get it done attitude. I mean I have exams as well but I would not mind
giving up an hour or 2 for a meeting to get ourselves oriented. It
would be a nice break from the textbooks and lecture recordings. But
just putting it out there my final exam is on December the 18th.
Ill post my thoughts on the CD a little later.
I have yet to look at the CD yet.
However for the meeting I think we should get it done as soon as
possible. For those of you who know me I kind of have that lets just
get it done attitude. I mean I have exams as well but I would not mind
giving up an hour or 2 for a meeting to get ourselves oriented. It
would be a nice break from the textbooks and lecture recordings. But
just putting it out there my final exam is on December the 18th.
Ill post my thoughts on the CD a little later.
gc
Nov 29, 2009, 10:44:09 AM11/29/09
to igemcanada
Good find Danielle! Andre, have you looked at the curriculum
section? There is a word document that could be useful. As for the
CD, it's very basic. Is it the whole CD or just a sample? Seems like
a lot of hype for what I saw on the CD. As for meeting, you'll just
have to propose a date/time. There aren't too many days that are
better or worse for me except that Tues are generally bad.
Cheers,
G.
section? There is a word document that could be useful. As for the
CD, it's very basic. Is it the whole CD or just a sample? Seems like
a lot of hype for what I saw on the CD. As for meeting, you'll just
have to propose a date/time. There aren't too many days that are
better or worse for me except that Tues are generally bad.
Cheers,
G.
Andre Masella
Dec 1, 2009, 9:42:08 AM12/1/09
to igemcanada
Okay,here is a Doodle: http://www.doodle.com/hatpzrt3nw4t3256
I'll pick a time on Friday. The first available time slot that
maximises the number of teams involved.
I still have not reviewed that CD. :-(
I'll pick a time on Friday. The first available time slot that
maximises the number of teams involved.
I still have not reviewed that CD. :-(
Eddie Yee Tak Ma
Dec 3, 2009, 9:03:43 AM12/3/09
to igemcanada
Hi all,
Here's a draft syllabus for the Practical Python for Biologist course
I'll be piloting at Waterloo next semester.
http://docs.google.com/Doc?docid=0Ae6vC6P08mfGZGc0MzI2N21fMjEwZGt2OWdiZmc&hl=en
Thanks,
Ed
Here's a draft syllabus for the Practical Python for Biologist course
I'll be piloting at Waterloo next semester.
http://docs.google.com/Doc?docid=0Ae6vC6P08mfGZGc0MzI2N21fMjEwZGt2OWdiZmc&hl=en
Thanks,
Ed
Andre Masella
Dec 3, 2009, 7:28:10 PM12/3/09
to igemcanada
> Good find Danielle! Andre, have you looked at the curriculum
> section? There is a word document that could be useful. As for the
> CD, it's very basic.
I've finally gotten a chance to sit down and look at this CD. I have
> section? There is a word document that could be useful. As for the
> CD, it's very basic.
two major criticisms: it is not presented any better than a standard
biology text (that is, the few animations don't compensate for the
fact that I'm mostly reading text from the screen) and it is not
presented in a way that is “for engineers” versus “for anyone who
doesn't know biology”. IMHO, one slide drawing analogies between DNA
and computer storage is not sufficient (nor relevant to, say, chemical
engineers).
Perhaps I am an egotistical idiot, but I think I can do better at an
explanation for engineers.
gc
Dec 3, 2009, 8:33:50 PM12/3/09
to igemcanada
Go for it. Just keep in mind it's only half the battle. You also
have to explain engineering to biologists!
G.
have to explain engineering to biologists!
G.
Andre Masella
Dec 4, 2009, 1:29:54 PM12/4/09
to igemcanada
We'll hold the meeting Monday Dec 7th at 1PM Eastern Time (11AM in
Alberta, 10AM in BC) using Skype. My Skype account is apmasell.
Alberta, 10AM in BC) using Skype. My Skype account is apmasell.
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