Re: [DIYbio] Digest for diybio@googlegroups.com - 25 Messages in 10 Topics

1:58 AM |

Hi,

For example I would love to have a reliable colony counter program.

The job there is to take an image, like this: http://x53.xanga.com/341f440279533263478321/b210037979.jpg and count how many spots are there on each plate. The program needs to count the spots, but needs to exclude air bubbles and other artifacts.

There are a few programs like this out there, but the ones I've tried give a lot of false positives and don't count the colonies very accurately. It can happen however that the perfect program exists, I just haven't tested it yet...


Secondly, I would be very grateful for a program that can identify homologous proteins in different organisms. The idea would be to give it either a DNA sequence, or a protein sequence and an organism. The program would then find other organisms which have the same gene, or a highly similar gene in them. So far there are numerous programs that can do this. But the problem is that distant relatives are not found after a while, as these programs always try to match new hits to the original sequence. So I would need a program that not only searches for homologs, but after it finds one, it matches new hits also to the newly found sequence. This way even distant relatives can be mapped. I do not know of such a program, but it can happen again, that this has been done by someone before...



On 29 June 2012 02:55, <diybio@googlegroups.com> wrote:

Group: http://groups.google.com/group/diybio/topics

    Mega <masterstorm123@gmail.com> Jun 28 07:32AM -0700  

    I'm also interested and wanna make some protoplasts some day... Maybe fuse
    an aplle tree with some tropical tree to make it winter-resistant and grow
    it in my garden :D
     
    That'd also be the first step to agrobacterium transformation...
     
     
     
    What I wonder:
    I buy some MS medium. Plate the tissue (cells) on it. Are the hormones for
    getting a whole plant (root formation, sprout,...) in the medium or do I
    have to add them later??
     
     
     
     
     
     
     
    Am Donnerstag, 28. Juni 2012 06:10:49 UTC+2 schrieb Ethan:

     

    phDIY <steve.frese@gmail.com> Jun 28 05:59AM -0700  

    Can you elaborate on your problems?
     
    On Wednesday, June 27, 2012 6:12:10 PM UTC-5, TRolandB wrote:

     

    TRolandB <williambeaufoy@gmail.com> Jun 28 04:43PM -0700  

    Hi there,
     
    The problem is that sometimes the procedure works and we get the correct
    bands showing up in electrophoresis, while other times we get no bands at
    all. We always follow the same general procedure, sometimes varying the
    quantities of reagents and PCR times to try and get it to work. Repeating
    the exact procedure from the times it did work doesn't lead to it working
    again.
     
    As the extraction process is the biggest variable we assume this is at
    fault. At the moment we extract it from cheek cells by scraping with a
    pipette tip. I've linked to the project page if anyone is interested, all
    info is there.
     
    http://wiki.london.hackspace.org.uk/view/Sex_typing_with_amelogenin
     
    Cheers
     
    Will
     
     
    On Thursday, 28 June 2012 13:59:39 UTC+1, phDIY wrote:

     

    Ethan <argentumxy@gmail.com> Jun 28 05:30PM -0700  

    Have you been running a ladder along with each gel or some other positive
    control? That would definitively tell you whether the error is in the
    extraction/PCR or the running/staining of the gels. What size is the
    fragment that you are trying to amplify? From my experiences, one hour at
    100V seems to be a fairly long time, but that might be the result of
    differences in fragment size that I have worked with and that you are
    trying to look at.
     
    As for tests with foodstuffs, I remember doing a PCR experiment in high
    school to test for the presence of a sequence that is commonly part of GMO
    crops. Unfortunately, I do not remember any of the specifics of what the
    sequence was.
     
    On Thursday, June 28, 2012 7:43:58 PM UTC-4, TRolandB wrote:

     

    Cory Tobin <cory.tobin@gmail.com> Jun 28 05:35PM -0700  

    The first step would be to really figure out which step is the
    problem. Have you tried doing multiple PCRs on the same DNA
    extraction?
     
    My suggestion would be to do 3 different DNA extractions all from the
    same person. Then do 3 different PCR reaction on each sample, mixing
    the PCR reagents separately for each reaction, then (assuming you are
    confident that your thermalcycler is consistent across wells) run all
    the reactions at the same time and then load them all into the same
    gel side by side. From there you should be able to tell if there is
    variability between extractions, between PCRs, or both.
     
    Also, what exact protocol are you using for the extraction? Your wiki
    links to a couple of different protocols. If you're using
    phenol/chloroform I would suggest doing multiple ethanol
    precipitations as phenol inhibits PCR.
     
     
    -cory

     

    Barra Darcy <baradarcy@gmail.com> Jun 28 07:32AM -0700  

    hmmm...
    I live in Ireland but would be going over to Indiana in August, I don't
    know if that's any help...it'd leave all the importation ('smuggling') up
    to me. I could send you the address if you have a e-mail?
    Is it only found over there or is this world-wide anyway?
     

     

    Giovanni Lostumbo <giovanni.lostumbo@gmail.com> Jun 28 11:36AM -0700  

    i also wanted to mention that the alternative transformation techniques use
    other patents outside of the Agrobacterium patent tree, though that's
    another long discussion.
     
    On Thursday, June 28, 2012 5:59:01 AM UTC-4, Giovanni Lostumbo wrote:

     

    CodonAUG <elsbernd@gmail.com> Jun 28 07:43AM -0700  

    The Google+ Hangouts are better than IRC for some things. Being able to
    have multiple simultaneous video feeds from multiple people would let the
    community share techniques, educate people, or just video chat.
     
    On Wednesday, June 27, 2012 8:38:13 AM UTC-7, Bryan Bishop wrote:

     

    Eugen Leitl <eugen@leitl.org> Jun 28 04:54PM +0200  

    On Thu, Jun 28, 2012 at 07:43:42AM -0700, CodonAUG wrote:
    > The Google+ Hangouts are better than IRC for some things. Being able to
     
    Except that they're a proprietary technology operated
    by an enterprise, and not open source protocols and implementations,
    run on own infrastructure.
     
    > have multiple simultaneous video feeds from multiple people would let the
    > community share techniques, educate people, or just video chat.
     
    I notice that top-posting and not trimming replies (message unchanged
    below) is also considered "better".

     
    --
    Eugen* Leitl <a href="http://leitl.org">leitl</a> http://leitl.org
    ______________________________________________________________
    ICBM: 48.07100, 11.36820 http://www.ativel.com http://postbiota.org
    8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE

     

    ruphos <apokruphos@gmail.com> Jun 28 09:52AM -0700  


    > Except that they're a proprietary technology operated
    > by an enterprise, and not open source protocols and implementations,
    > run on own infrastructure.
     
    Except that's philosophy and not a valid reason as to why a text based chat
    protocol is more helpful than multiple video streams.
     
     
    > > community share techniques, educate people, or just video chat.
     
    > I notice that top-posting and not trimming replies (message unchanged
    > below) is also considered "better".
     
    What, couldn't find a spelling error to critique?
     
     
     
    --
    "And if ye cannot be saints of knowledge, then be at least its warriors."
    -- Friedrich Nietzsche

     

    Eugen Leitl <eugen@leitl.org> Jun 28 07:02PM +0200  

    On Thu, Jun 28, 2012 at 09:52:21AM -0700, ruphos wrote:
     
    > Except that's philosophy and not a valid reason as to why a text based chat
     
    Politics, actually.
     
    > protocol is more helpful than multiple video streams.
     
    If you're using video for more than just talking heads you've
    got yourself a case. If not, not.

     
    > > I notice that top-posting and not trimming replies (message unchanged
    > > below) is also considered "better".
     
    > What, couldn't find a spelling error to critique?
     
    You've got the wrong nazi.

     

    phDIY <steve.frese@gmail.com> Jun 28 06:12AM -0700  

    If by synthetic organism, you mean one that's been completely generated
    from a computer (like at Synthetic Genomics) no.
     
    If you just mean bioengineered: you've already likely eaten a strain of
    streptococcus thermophilus or lactobacillus acidophilus (bugs used to make
    yogurt) that have been actively or passively engineered to produce that
    yogurt.
     
    as a microbiologist myself, I dont know if I would eat a bio-luminescent
    yogurt. There's no information on the allergenicity of the proteins used
    to make them glow. the GFP proteins are from jellyfish, originally, but
    have been substantially modified from their original form.
     
    On Wednesday, June 13, 2012 1:38:15 AM UTC-5, Jonathan Cline wrote:

     

    Barra Darcy <baradarcy@gmail.com> Jun 28 07:27AM -0700  

    I don't think eating anything GM is a good idea (but that's just my
    opinion...don't let me spoil the fun). I did hear a program on the radio a
    while ago, they were interviewing some scientist who worked with testing GM
    crops on mice. He said he'd filed some unpublished report that said the
    crop fed to mice had actually 're-arranged' their insides:-/
     
    but in the interests of science....

     

    Alex Hoekstra <alex.gmu@gmail.com> Jun 28 06:27AM -0700  

    Congratulations Ryan and Derek! Can't wait to see what you guys do now
    that you've got some resources to feed the dream.
     
    I'm a big fan of the Open Science Challenge, and hope it continues to grow
    and evolve in years to come. Some dreams must be fed.
     
    On Tuesday, June 26, 2012 2:39:47 PM UTC-4, Timothy Chen wrote:

     

    phDIY <steve.frese@gmail.com> Jun 28 06:02AM -0700  

    ClustalW is probably the way to go. BioEdit is a good program that you can
    use
     

     

    Alex Hoekstra <alex.gmu@gmail.com> Jun 28 06:08AM -0700  

    Congratulations indeed! When and where might we be able to watch?
     
    On Wednesday, June 27, 2012 7:48:49 PM UTC-4, Avery wrote:

     

    "Günther Mulder" <guenther.mulder@gmail.com> Jun 28 01:52AM -0700  

    Hi
     
    so what kind of software do you need most, well, desparately?
     
    On Wednesday, 20 June 2012 11:05:25 UTC+2, Ravasz wrote:

     

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