As a bio-noob, where do I start learning?

[Dirk Broenink]

From what I've read so far, DIYbio seems really interesting and full of potential. I want to know more about it. If I could at least understand more of what is being said here that would already be helpful.

I'm a computer scientist, but the same goes for people from other professions, where to start learning?

Suggested resources (tutorials, books, articles, videos) are welcome.

[Nathan McCorkle]

diyhpl.us/wiki/diybio/
http://openwetware.org/wiki/DIYbio/FAQ
http://openwetware.org/wiki/Main_Page

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-Nathan

[Nathan McCorkle]

Spend a bunch of time scanning for keywords and googling them,
University will teach you to memorize all the terms, but you could
also just google everything all the time. For a starter project you
could even try writing a de-jargonizer... something that takes a block
of text and replaces jargon with their definitions. (Not sure that'd
be worth it, but it'd be interesting to try)

--
-Nathan

[William Heath]

Hi Dirk,

Try to reproduce all iGem experiments both simulated and in the lab proper.

-Tim

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CA%2B82U9KyVVffJA7bz8w9goSL0JtRn1QxPyrRNnkF1JTO3oL2Tw%40mail.gmail.com.

[Heather Dewey-Hagborg]

Take a class! Hands on is the best way to learn I think. Check out Genspace for example. (Depending on where you are located of course).

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Heather Dewey-Hagborg

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[Nathan McCorkle]

Even community college labs can be VERY well equipped. For the number
of hours spent in lab, they're quite cheap per-hour. You can likely
even find some classes that you can take aside from the lecture, if
you tell them you don't want the credit (paid auditing?).

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-Nathan

[Yunfan Jiang]

your situation is same as me, i am a programmer and also a bio-noob, i am currently learning basic bio from an paper version turtorial

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Name: yunfan
Site: http://geek42.info/
Interest:
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[Alexey Zaytsev]

I used to be a software developer, now a masters student in Systems and Synthetic biology. I would suggest:

- Khan Academy.

- The 7.00x course at EdX, it's awesome.

- Any other biology-related courses on Coursera/EdX/etc, sign up, but don't waste your time if you feel the course is either bad of not at your level.

- Of course, wikipedia, books, and you will figure it out.

Well, that's if you want to know more about molecular biology, and not just follow through some simple experiments without understanding what's going on.

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[William Heath]

Alexey,

What is it like to make the transition from Computer Science to Systems and Synthetic Biology?!!!  Give me some clear insights using computer science terminology if you would be so inclined!

-Tim

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[Alexey Zaytsev]

In computer science terminology, it's awesome.

It's like when I was a kid trying to make sense of a computer, except cells are not quite like computers, and don't always work, and almost never work in the way you want them to. But when they do, it's certainly awesome.

But being honest, the level of complexity of the stuff we can design to be put into cells right now is more on the level of electronics ~ 100 years ago - not exactly computer age. It's not programming - more like trying to design a new circuit with a couple vacume tubes and a few passive components, using math and best guess. And DIYbio? More like connecting a light bulb to a battery - still awesome, if you consider that people only started seeing electricity as something practical 30 years ago, and now you can create light, without a candle, yourself, at home!

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CAAcUL6m4auMUqT2w5NSKGjgK6U4uTq%2B%3DAAE-MjXVEN-qpu5xXg%40mail.gmail.com.

[Nathan McCorkle]

On Mon, Feb 24, 2014 at 7:42 PM, Alexey Zaytsev
<alexey....@gmail.com> wrote:
> In computer science terminology, it's awesome.
>
> It's like when I was a kid trying to make sense of a computer, except cells
> are not quite like computers, and don't always work, and almost never work
> in the way you want them to. But when they do, it's certainly awesome.
>
> But being honest, the level of complexity of the stuff we can design to be
> put into cells right now is more on the level of electronics ~ 100 years ago
> - not exactly computer age. It's not programming - more like trying to
> design a new circuit with a couple vacume tubes and a few passive
> components, using math and best guess. And DIYbio? More like connecting a
> light bulb to a battery - still awesome,

I think it really depends more on initiative and self-determination.
Mega (Andreas) is the first 'poster-child' that comes to mind for this
sort of thing, he did (and does) exactly what I tell all new-comers
here... don't stop reading and keep asking questions. There are easily
50 to 150 person-years worth of core-science academic
university-learned people on this list who are active quite often.
Some of these people have quite an in-depth and multi-discipline
experience and expertise. Genspace and Biocurious hackerspace-type
places would be more like satellite campuses of DIYbio... but most of
the work with molbio/biotech/chem is mental. You can not ever stop
reading because there are 1000s of years of relevant tips and tricks
and crap that went wrong that can help you, and more of that being
created every day. You need to learn how to read papers and how to
separate facts from opinions, how to scan quickly for information by
using keywords such as units (Seconds, Hz, Volts, millimeter) because
you don't have forever to sort through every word of a paper or book
to determine it doesn't have the answer you're looking for and it was
actually a waste of time reading it.

Are people just not driven enough, or don't know how to communicate,
don't know how to type on a keyboard, I'm not sure... no one here
get's annoyed with questions and comments, ask as many questions and
post all your findings until your fingers hurt from typing.

[Cathal Garvey]

The Synbio:Electronics comparison I'll agree with. To describe DIYbio as
the childlike equivalent is, I think, a disservice. Yes, we start out
that way, but so do academically-trained folk; learning 'dumb'
experiments in teaching labs.

I think the big reason we're mostly stuck with primitive experiments is
that we don't have access to the awesome bits we need to do better.
That's instruments, certainly, but we've spent the last few years either
rewriting the protocol book to remove missing equipment and chemicals,
or designing cheap equipment we can all afford.

I think we're now on the cusp of tackling the other missing ingredient;
the DNA. When we've all got access to good fundamental DNA on which we
can build, I think we'll start seeing what all the last few years was
worth in terms of complexity and creativity in DIY-synbio.

At least, I hope we're at that point; sort of gambling on it, in fact.
:) I can't think what other missing ingredient we're really suffering
for, now that we can all access DNA synthesis services, software, and
the hardware and methods to use it all? Roll on DIY-synbio?

>> https://groups.google.com/d/msgid/diybio/CAAcUL6m4auMUqT2w5NSKGjgK6U4uTq%2B%3DAAE-MjXVEN-qpu5xXg%40mail.gmail.com
>> .

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Please help support my crowdfunding campaign, IndieBB: Currently at
27.7% of funding goal, with 17 days left:
http://igg.me/at/yourfirstgmo/x/4252296
T: @onetruecathal, @IndieBBDNA
P: +3538763663185
W: http://indiebiotech.com

[Dakota Hamill]

I don't think lack of enthusiasm or drive is a problem, from where I stand, it's lack of equipment and space that is the biggest issue.  Many people, myself included, are in tens of thousands of dollars of debt from school, and have to balance finding money for food and an apartment with money for consumables and equipment.  That being the case, a 9-5 job is needed, which generally ends up being a 9-7 job, which completely sucks your energy during the week and makes weekends the more favorable time to be in the lab.  Couple that with heading to the lab to do an experiment and realizing you don't have that one extra piece of equipment you need, or that reagent you need but can't get because Sigma won't ship it to you, and it's really damn frustrating.

What's the alternative?  Go to grad school and slave for 5 years so your PI can take credit for any work you do?

In the end, I guess these are all just excuses.  If I wanted it bad enough I'd sell a kidney and sleep in a van and work 25 hours a day.

[Alex]

+1 to your entire email.

The only other thing I have to add is that it's difficult to find relevant reading materials. I'm a complete noob, if I were to go read about the stuff that is generally discussed on this list, it'd be waaay above my head 80% of the time. At the same time, being interested in plants, I'm starting with a plant biology book. However, it is heavy with a lot of info that, without guidance, I'm not sure is relevant at all. For all I know, I'll spend 2 months trudging through this data and come out equally clueless.

I'm aware this may also be a flaw on my behalf in someway I'm not saying that everyone would have this issue and, for all I know, I may get through this and be much more  knowledgeable. I'm simply saying that I can feel the pain here as well!

This group does help immensely though, if not just to continuously peak my interest!

Alex

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[Cathal Garvey]

I'd probably have had better luck crowdfunding a beginner's book, it
seems. I've talked about it before but never completed even the
introduction chapter; if I run out of cash and can't do open-source DNA
development anymore, I'll give it another shot.

Please don't take that as motive to sink my current project, though; I
really do prefer making things to writing about it! :)

[Alexey Zaytsev]

I didn't say it's all childs play. ;)

Ok, now is 1914. Most people not living under a rock have hard about that electricity thing, that it can kill you, is expensive to produce, can be used to make light, and even lets you send telegrams. You've probably heard about the radio as well, but sending wireless telegrams? That's just magic. The engineers are busy inventing the amplifiers and modulators that could be used to broadcast human voice over a significant distance, bu that's something way out of an individuals reach for the moment, unless you are ready to invest a lot.

You are a mechanical engineer - gears, nuts, new machining methods, plenty of opportunities to apply your skills. They mentioned that electricity thing in the phisics class in school years ago, and even performed some experiments that involved sparks, but that stuff's just evolving so quickly and is all over the news (journalists writing utter bullshit as usual). So you are curious, are able to find some basic information on how it actually works, and want to try. You are able to buy a small light bulb - still quite expensive, but that's pretty hi-tech, with good vacume and a super-tiny fillament inside. For the electricity source, you use some copper coocware and zink sraps to build a Daniell cell. You struggle to get the damn thing working for about a month, try different designs, learn a bit of chemistry, and one evenig, you connect your light bulb and see the filement light up - wohoo!

[Alex]

I like your current campaign but have been unable to pledge due to funding (fitting Dakota's desc to a T) and, for me, I'm not sure how beneficial it would be, being so new to this all. I mean no disrespect with that  statement. I'm just saying that, at my current level of understanding, the experiment would be interesting but I need to start smaller.

However, I'd definitely be willing to pledge to a reasonably priced beginner's book! The benefit could easily justify my pledge there, assuming that it's well written!

Alex

[Cathal Garvey]

Well, considering IndieBB is supposed to come with a full-colour
instruction book for absolute beginners, I'll be writing it up to some
extent one way or another.

I had intended this to be a total-beginner's kit that teaches
sterilisation, bacterial handling, and then manipulation, in a one-step
crash-course. I'd like to know what I can do to make that more appealing
and less intimidating to you as a beginner?

Of course, I totally understand if it's a simple issue of not having
enough money to invest in stuff. With any luck if it works out you'll
have a friend to give you a copy! ;)

Maybe I should put up a new pledge: "buy one, give one"? :)

[John Griessen]

On 02/25/2014 11:28 AM, Cathal Garvey wrote:
> I had intended this to be a total-beginner's kit that teaches
> sterilisation, bacterial handling, and then manipulation, in a one-step
> crash-course.

Oh, then that is a big bragging point that needs to be spelled out also.

[Alex]

It's definitely more a monetary issue than anything else.

Timing wise, I think if it would've come around in a couple years I may have been more likely to pledge. With my current focus being to learn the inner workings of plants from a life science/life cycle/cellular perspective, a jump into Synthetic bio seems a large one. That's not to say that, given the funds, I wouldn't have pledged because I surely would have.

Just, in my current funding situation, given the cost of the kit, I can't justify it. My thought with the theoretical book campaign was that it would be more generic so I may have misunderstood your intentions there.

Sorry, that probably doesn't help much but, in my case at least, I don't think that it's an issue on your side. Just more of a situational issue.

Alex

[Lisa Thalheim]

I'd like to see more beginner's books as much as the next person.

Until then, there are some books out there that are pretty neat to get
started with the hands-on part. Some of my favourites:

Molecular biology: A Project Approach by Karcher
I, Microbiologist by Sanders-Lorenz and Miller
Illustrated Guide to Home Biology Experiments by Thompson and Thompson
Plant Tissue Culture: Techniques and Experiments by Smith
At the Bench: A Laboratory Navigator by Barker

If you read German, the "Experimentator" series is also pretty great, as
is "Mikrobiologische Methoden" by Bast.

Not quite as hands-on, but a very expansive and accessible read to get
some context and background:

Molecular Biotechnology by Pasternak and Glick

I'm sure there are tons more out there.

Cheers,
Lisa

[Mega [Andreas Stuermer]]

I'm compiling a noob guide at the moment (but it is moving very slow, 1000s of other things to do)

I want to attach pictures soon, but I cannot just take some from google - someone will sue me if I publish it. So I gotta draw them myself

Find some raw material attached.

[Mega [Andreas Stuermer]]

Just improved it a bit

Am Montag, 24. Februar 2014 23:56:49 UTC+1 schrieb Dirk Broenink:

[Dirk Broenink]

That's great, thanks! It explained it to me on just the right level of complexity. 

[Mega [Andreas Stuermer]]

Great to hear that ;) I may draw pictures some time to better show it...