Tips for the new guy, so he can avoid posting stupid questions.

[Avery Ashley]

Hey guys, I'm relatively new to this. I'm only in my second year at college (community college at that), but I have a passion for biology, lots of free time and a little money free to spend on a good hobby.

I've never worked in a real lab, so there's a lot of techniques I need to learn and I don't want to be constantly posting here about them and wasting your time. 

I've gotten a makeshift incubator and centrifuge, and a legit thermocycler and electrophoresis chamber but I really don't know how to use any of it very well.

Basically, I have everything I need I just need to learn how to use it properly.

I want to work mostly  on plants, and my goal is to be able to insert genes in them by the end of summer (not to accomplish anything really, just be able to do it).

Where do i start?

I have a relatively firm understanding of basic biology and biochemistry, I'm only looking for a place to learn lab technique.

And I'm pretty much stuck on my computer.

Thanks for the help, you guys are one of the most understanding and helpful community's I've ever encountered on the internet, and I'm proud to be a part of all this.

[Dakota Hamill]

I'll try to find some more things tomorrow, but I found this website really nice, and stumbled on it a year or two ago.  What thermal cycler and gel box did you end up going with?

http://www.benchfly.com/

It's basically youtube, but ALL lab techniques.  Sometimes you can find good stuff on youtube, or MIT open course ware, but some times on youtube it's explained poorly, or it's just text layed over a video and not really informative.  Most of the videos I've seen on benchfly can be really detailed and informative, and explain not just how to do something, but why you do certain things (all the ins and outs and nuances) 

[Avery Ashley]

Thanks for the reply, I'll check it out.

I bought a used perkin gene amp 2400. I guess I should have said the chamber is makeshift too, its just a little plexiglass box with battery hooks, not even sure if it'll work haha.

[Avery Ashley]

Also, I want to invest in a good pipetter, is there a good "do it all" one (maybe interchangeable tips) so I don't have to buy multiples?

[Sebastian S. Cocioba]

If you really feel out of your element and want kind of a guiding hand, edvotek sells kits that range from bacterial transformations to gene amplification, ligations, etc. The cost is obviously more than getting the disposables/ingredients yourself but the packaged convenience is worth it IMO. Sometimes, by not knowing what you need, you end up overspending on raw materials. Amazon.com has an edvotek listing in case they wont ship to your address. They mostly deal with schools so the listing is a work-around. The alternative to kits would be much more time consuming since you would have to learn what everything does and how much you need and most importantly why on your own. The internet is a beautiful place. If you have the time you can learn everything you need at the click of a mouse. Benchfly is great. Jove has some public access videos too. Its like a research article but in video format which may be helpful at times. Openwetware is another great resource. And of course just ask the list. If you just try to do a google search on the topic before posting, you might either find your answer or narrow your question significantly. If not then ask away. There are tons of people who enjoy helping others in this community. We all had to start somewhere! :) good luck!

PS: nice buy on the gene amp. I got its grandfather the 9600. What a giant machine! As long as it gets the job done, eh? :)

Sebastian S Cocioba

CEO & Founder

New York Botanics, LLC

Sent via Mobile E-Mail 

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[Avery Ashley]

Thanks for the reply! I checked out some of their stuff, and I think I'll pick up a kit just to get started with. 

[Sebastian S. Cocioba]

The wider the range it covers, the bigger the error. Normally a set of 1-10 10-100 and 100-1000uL works best. If you get gilson pipettemen u can use two tips for three pipettes. Ebay offers sets for cheap. If you have to buy new there is a sale on accupet pipettors for 119 a pop at pipette.com. They are decent and i use them and never had an issue. I know its pricey but its the most important tool in your lab, second only to your eyes, hands, and mind.

Sebastian S Cocioba

CEO & Founder

New York Botanics, LLC

Sent via Mobile E-Mail 

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[Koeng]

I was in the same boat as you once, except until recently I haven't discovered DIYbio so all I had to guide me is the experiment I wanted to complete and a computer to sit hours upon hours infront. I don't have a firm understanding of most complex biology/biochemistry, I haven't even passed high school! Lab technique is what I do know :). But I just set a goal on something cool and began collecting things.

My recommendation- Just get a goal and start. Start getting decent equipment as the experiment needs. I got my plasmids from Carolina, cheap and easy, even though I only got pGreen and pVIB. When I started transformations I didn't even have a water bath, or an incubator, or pipettes. I didn't even have a metal inoculating loop! But to make transformations easier, I started to get these things. Then it just started piling up and I got into viruses, then where I am now, plasmids. Also, get GOOD, let me repeat this GOOD LB agar. Make your own! Do anything and avoid buying it from p212121 (They have great regents, just check out GoldBio first). Mine sucks and that, strangely, is the biggest thing holding me back from most my experiments. GET GOOD AGAR PLATES

Some software to get: ApE and SnapGene. ApE is great for making DNA because it is almost like a text editor, and snapgene is just so easy! I highly recommend the free trial when you start your first major project.

Mo bio: This is where you can make a living getting samples. For that reason I always buy from them because I get to try their products first. This can supply you for quite a while.

And finally I will try to keep up about plant transformation. I want to try it too :)
-Koeng

[Avery louie]

Just a plug for one of our fellow DIYBIO folks, Mac Cowell sells super affordable pipettors.  They should be worth a shot- they are very competitively priced: super affordable pipettors.  Your other best bet is to get a set of gilsons (kind of the mo-bio standard) off ebay.

--Avery

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[Sebastian S. Cocioba]

Wow thats a fantastic price! Is the catch just that its OEM? Either way as a beginner set thats wonderful. Three pipettors for the price of an okay one on sale. If I had a time machine...:P

Sebastian S Cocioba

CEO & Founder

New York Botanics, LLC

Sent via Mobile E-Mail 

[Avery louie]

OEM?

[Sebastian S. Cocioba]

Original equipment manufacturer. Its made in china but via ISO standards so I would not worry. Normally if you buy a product straight from the source its cheaper but when the source is China people tend to think cheap and flimsy. If these really are able to match the ISO standards then I am down to buy a whole set...

Sebastian S Cocioba

CEO & Founder

New York Botanics, LLC

Sent via Mobile E-Mail 

[Avery louie]

Ah.  Right.  There are two definitions.  In the automotive world, OEM generally is the better thing to get- because it is the actual part made by say, Ford.  An exact replacement.  The other definition confuses me...

I think they are worth looking into.  I have never held one, but if you need to go for cheap pipettors, or you need lots, I would check it out.  He even gives a discount for a set of 3- $125 for the whole set, if i do my math right.  It's also a DIYBIO company, FWIW (in my book, important).

--A

[Mac Cowell]

Hey everybody, Mac here. I run genefoo.com and sell the fabulous $44 pipettes.  If you buy a box, you will see the are marked as "The Ultimate Pipetting Experience" :)  I'm happy at least to sell them at the ultimate price.  It's up to you to decide if it really is the ultimate pipetting experience :)  

As Sebastian suggested, I import them from Shanghai.  So far, they seem great.  I am still trying to figure out the design pedigree of them, but I think they are based on finnpettes from the 90s.

My goal with genefoo is to lower the barrier to entry for a lot of basic molecular bio lab equipment, in an open-source way when possible, and these pipettes are genefoo's first product.  Rest assured that if they don't work for you, I will do everything it takes to make them better, and together we'll find the best pipettes for diybiologists.  Maybe importing them won't even make sense in the long run and used sets from ebay will be the best way to acquire them for users on a shoestring budget.  Time will tell, and it will tell faster with your help.

By the way, I want to offer a 5% discount on a set of 4 pipettes,  Please email me at sa...@genefoo.com to set that up.

Cheers

Mac

[Cathal Garvey]

How did I miss genefoo?!
Sign me up for a 4-pack! :D
(Posting in offline mode, will hit up genefoo ASAP and place an
order..assuming you guys can ship overseas!)

On 28/01/13 05:51, Mac Cowell wrote:
> Hey everybody, Mac here. I run genefoo.com <http://genefoo.com> and sell

> the fabulous $44 pipettes. If you buy a box, you will see the are
> marked as "The Ultimate Pipetting Experience" :) I'm happy at least to
> sell them at the ultimate price. It's up to you to decide if it really
> is the ultimate pipetting experience :)
>
> As Sebastian suggested, I import them from Shanghai. So far, they seem
> great. I am still trying to figure out the design pedigree of them, but
> I think they are based on finnpettes from the 90s.
>
> My goal with genefoo is to lower the barrier to entry for a lot of basic
> molecular bio lab equipment, in an open-source way when possible, and
> these pipettes are genefoo's first product. Rest assured that if they
> don't work for you, I will do everything it takes to make them better,
> and together we'll find the best pipettes for diybiologists. Maybe
> importing them won't even make sense in the long run and used sets from
> ebay will be the best way to acquire them for users on a shoestring
> budget. Time will tell, and it will tell faster with your help.
>
> By the way, I want to offer a 5% discount on a set of 4 pipettes,

> Please email me at sa...@genefoo.com <mailto:sa...@genefoo.com> to set

> that up.
>
> Cheers
> Mac
>
>
> On Sun, Jan 27, 2013 at 9:26 PM, Sebastian S. Cocioba
> <scoc...@gmail.com <mailto:scoc...@gmail.com>> wrote:
>
> Original equipment manufacturer. Its made in china but via ISO
> standards so I would not worry. Normally if you buy a product
> straight from the source its cheaper but when the source is China
> people tend to think cheap and flimsy. If these really are able to
> match the ISO standards then I am down to buy a whole set...
>
>
> Sebastian S Cocioba
> CEO & Founder
> New York Botanics, LLC
>
> Sent via Mobile E-Mail
>
> On Jan 28, 2013, at 12:23 AM, Avery louie <inact...@gmail.com

> <mailto:inact...@gmail.com>> wrote:
>
>> OEM?
>>
>> On Mon, Jan 28, 2013 at 12:20 AM, Sebastian S. Cocioba
>> <scoc...@gmail.com <mailto:scoc...@gmail.com>> wrote:
>>
>> Wow thats a fantastic price! Is the catch just that its OEM?
>> Either way as a beginner set thats wonderful. Three pipettors
>> for the price of an okay one on sale. If I had a time machine...:P
>>
>>
>> Sebastian S Cocioba
>> CEO & Founder
>> New York Botanics, LLC
>>
>> Sent via Mobile E-Mail
>>
>> On Jan 28, 2013, at 12:15 AM, Avery louie

>> <inact...@gmail.com <mailto:inact...@gmail.com>> wrote:
>>
>>> Just a plug for one of our fellow DIYBIO folks, Mac Cowell
>>> sells super affordable pipettors. They should be worth a
>>> shot- they are very competitively priced: super affordable

>>> pipettors <http://genefoo.com/products/pipettes>. Your other
>>> best bet is to get a /set/ of gilsons (kind of the mo-bio

>>> <mailto:diy...@googlegroups.com>. To unsubscribe from

>>> this group, send email to
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[Cathal Garvey]

Hi Mac,
Request #1: Remove need for ZIP codes for Ireland! We don't have any! ;)

On 28/01/13 05:51, Mac Cowell wrote:

> Hey everybody, Mac here. I run genefoo.com <http://genefoo.com> and sell

> the fabulous $44 pipettes. If you buy a box, you will see the are
> marked as "The Ultimate Pipetting Experience" :) I'm happy at least to
> sell them at the ultimate price. It's up to you to decide if it really
> is the ultimate pipetting experience :)
>
> As Sebastian suggested, I import them from Shanghai. So far, they seem
> great. I am still trying to figure out the design pedigree of them, but
> I think they are based on finnpettes from the 90s.
>
> My goal with genefoo is to lower the barrier to entry for a lot of basic
> molecular bio lab equipment, in an open-source way when possible, and
> these pipettes are genefoo's first product. Rest assured that if they
> don't work for you, I will do everything it takes to make them better,
> and together we'll find the best pipettes for diybiologists. Maybe
> importing them won't even make sense in the long run and used sets from
> ebay will be the best way to acquire them for users on a shoestring
> budget. Time will tell, and it will tell faster with your help.
>
> By the way, I want to offer a 5% discount on a set of 4 pipettes,

> Please email me at sa...@genefoo.com <mailto:sa...@genefoo.com> to set

> that up.
>
> Cheers
> Mac
>
>
> On Sun, Jan 27, 2013 at 9:26 PM, Sebastian S. Cocioba
> <scoc...@gmail.com <mailto:scoc...@gmail.com>> wrote:
>
> Original equipment manufacturer. Its made in china but via ISO
> standards so I would not worry. Normally if you buy a product
> straight from the source its cheaper but when the source is China
> people tend to think cheap and flimsy. If these really are able to
> match the ISO standards then I am down to buy a whole set...
>
>
> Sebastian S Cocioba
> CEO & Founder
> New York Botanics, LLC
>
> Sent via Mobile E-Mail
>
> On Jan 28, 2013, at 12:23 AM, Avery louie <inact...@gmail.com

> <mailto:inact...@gmail.com>> wrote:
>
>> OEM?
>>
>> On Mon, Jan 28, 2013 at 12:20 AM, Sebastian S. Cocioba
>> <scoc...@gmail.com <mailto:scoc...@gmail.com>> wrote:
>>
>> Wow thats a fantastic price! Is the catch just that its OEM?
>> Either way as a beginner set thats wonderful. Three pipettors
>> for the price of an okay one on sale. If I had a time machine...:P
>>
>>
>> Sebastian S Cocioba
>> CEO & Founder
>> New York Botanics, LLC
>>
>> Sent via Mobile E-Mail
>>
>> On Jan 28, 2013, at 12:15 AM, Avery louie

>> <inact...@gmail.com <mailto:inact...@gmail.com>> wrote:
>>
>>> Just a plug for one of our fellow DIYBIO folks, Mac Cowell
>>> sells super affordable pipettors. They should be worth a
>>> shot- they are very competitively priced: super affordable

>>> pipettors <http://genefoo.com/products/pipettes>. Your other
>>> best bet is to get a /set/ of gilsons (kind of the mo-bio

>>> <mailto:diy...@googlegroups.com>. To unsubscribe from

>>> this group, send email to
>>> diybio+un...@googlegroups.com

>>> <mailto:diybio%2Bunsu...@googlegroups.com>. For more

>>> options, visit this group at
>>> https://groups.google.com/d/forum/diybio?hl=en

>>> Learn more at www.diybio.org <http://www.diybio.org>

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>>> For more options, visit
>>> https://groups.google.com/groups/opt_out.
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>>>
>>>
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[Avery Ashley]

I got up with an Edvotek rep to see if they would sell me reduced kits (because the smallest kits are for a classroom of 10), and they sent me this back.

Hi Avery,

I'm glad to hear that we have plenty of products that you're interested
in! If you have extra agarose, buffer and stain we can supply the other
reagents at a discount for the kits you've listed.

Thanks,

-Jeff

These are the kits I listed:

 Mini-Prep Isolation of Plasmid DNA

 Isolation of E. coli Chromosomal DNA 

Cleavage of DNA with Restriction Enzymes 

 

 

PCR Amplification of DNA                                   

DNA Fingerprinting Using Restriction Enzymes 

Transformation of E. coli with Blue and Green Fluorescent Proteins 

 Quick Plant Genetics Using PCR

Sounds like I might be able to get a good deal.

Only problem is, I don't really know what the other reagents I need are, and I'm also not sure what kind of buffer, agarose and stain I would need (That's what I was going to buy the kit to figure out).

Would you mind giving me a few pointers?

I hate to be a leach on the community, I promise I'll return all these favors later on when I'm knowledgeable enough to do so.

[Dakota Hamill]

Hi, don't feel like you are a leach, the whole point of this list is to share info!

In fact, you may have stumbled upon something here.  In your next email to them, if all goes well, maybe you could mention the DIY list and that you may be sending more potential customers to them, and maybe they could setup a coupon sort of deal...or have some way of knowing that if you list DIYBio, you can buy kits with enough materials for 1-2 reactions per kit instead of the full 10.  Might as well have 1 or 2 extra rxns in case one messes up.

I'd be interested in that blue and green protein transformation to be honest.

It seems like all the kits come with the required things...but maybe they are reducing the price with the forethought that you already have agar to pour gels, or a DNA stain to use (since multiple kits use the stain).  I'm a little confused to, they weren't specific on what exactly they'd give you with the reduced price.

A good buffer to have on hand is TBE or TAE, used for pouring and running gels, it's pretty cheap.  You can stain gels with methylene blue for white light visualization, or GelGreen or SYBRGreen for LED/UV visualization.

If I'm not mistaken methylene blue stain usually takes a few hours to overnight to visualize the DNA, I've got GelGreen which worked fantastic for UV illumation, and I know others have had success with blue LED illumination but I"ve yet to get a blue LED.

I can't find all the links atm but, my most recent purchases have been from

http://www.phenixresearch.com/products/lab-supplies.asp

for GelGreen, and agarose.  You might also find your tubes, tips, EDTA, tris, or premade TBE or TAE on there as well.

Maybe try to get prices for 2-3rnx per kit, and ask if they'd still provide everything they say they will on the kits main page, just in smaller quantities. 

[John Griessen]

On 01/28/2013 05:11 AM, Cathal Garvey wrote:
> How did I miss genefoo?!
> Sign me up for a 4-pack! :D
> (Posting in offline mode, will hit up genefoo ASAP and place an
> order..assuming you guys can ship overseas!)

Well since they already traveled over big seas, we assume yes.

I searched out Mac's likely source and they make all kinds of standard lab gear.
Makes me think my aim to combine standard operations with automation
is right, and the only thing that will compete against Chinese suppliers
"for a while", and then innovate again or die, open-hardware-business-wise.

[Nathan McCorkle]

On Mon, Jan 28, 2013 at 4:36 PM, John Griessen <jo...@industromatic.com> wrote:
> Well since they already traveled over big seas, we assume yes.
>

When the trans-asian railway is finally working right, shipping to
Ireland from China should be significantly cheaper than it currently
is. (current too many different rail gauges currently cause a major
PITA, thus most goods travel from China to the west by boat)

> I searched out Mac's likely source and they make all kinds of standard lab
> gear.
> Makes me think my aim to combine standard operations with automation
> is right, and the only thing that will compete against Chinese suppliers
> "for a while", and then innovate again or die, open-hardware-business-wise.
>

AliBaba or AliExpress have lots of pipette suppliers, but Mac and
others will be able to out-compete because they know English quite
well. I've dealt with several companies on the Alis, and English
competency is far below what I expected for the tech sector. They've
even had problems understanding that multiple orders could be combined
in one shipping box, to save them shipping, and minimizing order
completion time.

Just because something is ISO9001 doesn't mean they can communicate
with you, and doesn't mean they do much Quality Control or
characterization Even if they do QC and have "professional" item
characterization (i.e. data sheet), it's definitely not the same as
what you get from most of the well-established USA/EU companies. For
pipettes this might not be a big deal, but what about the purity of
that lab reagent?

--
-Nathan