Online Course: Introduction to DNA Barcoding ---> Other DNA analysis MOOCs?

[Jason Bobe]

University of Guelph is offering a new online course: Introduction to DNA Barcoding:

http://dnabarcodingcourses.com/course-description/#.html

Tuition is ~$1000.  

Anyone know of any good DNA analysis MOOCs available out there?

Jason Bobe

[Ashley Heath]

Ouch!

[SC]

$1000 for an *online* course?  Seems a tad steep.

Extensive info on the hows and whys of barcoding is freely available on the web.

 

 

[Nathan McCorkle]

What's a MOOC?

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[Dan]

massive open online course MOOC

I'm taking a coursera course on epigenetics taught by an appealing Australian professor. It is excellent. Virology starts August 1. All are free. I am waiting for the tissue engineering course to start.

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CA%2B82U9K5sYf%2BOxjujk1%2BDYB4ReGztymJCU24wj6T3bnww4QzKQ%40mail.gmail.com.

[jlund256]

If you can work without the structure of a course, you can learn about as much by visiting the Barcode of Life site and reading the information they have: http://www.barcodeoflife.org/content/about/what-dna-barcoding

Also, they link to pdfs of a bunch of DNA barcoding papers, I would start with the reviews:

http://www.barcodeoflife.org/content/resources/publications?perpage=all

Jim Lund

[Destiny Z]

Hey Roninlaw, I'm taking that epigenetics course too! I agree, I think it's very well put together and is turning out to be an excellent course.

I'm also taking the course Computational Molecular Evolution taught out of Denmark. I think that MOOCs are a great place to learn computer basses disciplines, and I wanted to see that applied to biology. So far it's going pretty good, and I'm learning more about how to make phylogenetic trees than I ever was taught during my undergrad.

I just really wish they had a class on using software to analyze DNA sequences. I am learning that a bit though my current class, but I would really like to see a course dedicated to using and understanding BLAST and other analysis programs.

[ndpm]

It was mentioned here once before (last year) but those interested in bioinformatics and sequence analysis might like ROSALIND, a site with a series of problems to be solved using any programming language of your choice. The problems start out easy and get harder. There is no instruction, but for a self-learner it's pretty cool.

http://rosalind.info

[Nathaniel Chen]

> It was mentioned here once before (last year) but those interested in bioinformatics and sequence analysis might like ROSALIND, a site with a series of problems to be solved using any programming language of > your choice. The problems start out easy and get harder. There is no instruction, but for a self-learner it's pretty cool. http://rosalind.info

Wow, this looks awesome! Like Project Euler for bioinformatics.

MIT Open Courseware has a broad biology section, including some computational biology courses:

http://ocw.mit.edu/courses/find-by-topic/

[Destiny Z]

ndpm, that's so cool!

I've been learning python on my own time through codeacademy, and it's going to be a huge boon to me to use that in a sequence analysis context. Thanks so much for sharing that link!

[Jason Bobe]

On Wednesday, July 24, 2013 2:10:01 PM UTC-4, Nathan McCorkle wrote:

What's a MOOC?

here is a MOOC on genomics at udacity: "Tales from the genome"

https://www.udacity.com/course/bio110

Lesson 1: Introduction to traits and heredity

Trait variation and categorization, basic models of inheritance, and the connection via DNA. Check out the concept map for this lesson.

Lesson 2: Defining the genome

DNA structure, chromosomes, and genome organization. Check out the concept map for this lesson.

Lesson 3: How a genome works

Protein coding genes, transcription, translation, discerning the genetic code, and alleles. Check out the concept map for this lesson.

Lesson 4: Gene regulation

Non-coding DNA, regulatory regions of genes, and transcription factors. Check out the concept map for this lesson.

Lesson 5: Transmission of genes and traits

Family relationships and pedigrees, inheritance patterns, allele dominance, and chromosome dynamics.

Lesson 6: Origin of mutation/variation

Types of mutations, various causes of mutation, allelic frequency, and the spread of alleles in a population

Lesson 7: How to obtain and interpret genomic information

Personalized genetics: sample acquisition, DNA extraction and processing, and interpretation of results

Lesson 8: Simple genetic traits

Molecular causes of monogenic traits, loss-of-function vs. gain-of-function alleles, and dominance.

Lesson 9: Multifactorial traits

Polygenic traits, complex traits with an environmental effect, qualitative and quantitative measures, twin studies, relative risk, and genome-wide association studies (GWAs)

Lesson 10: Pharmacogenetics: genes and drugs

Pharmacokinetics and pharmacodynamics, alleles affecting drug metabolism, and personalized medicine

Lesson 11: Human ancestry and evolution

Identity by state (IBS), Identity by descent (IBD), relative finder, maternal and paternal lineages, neanderthal interbreeding, and human/chimp evolution

Lesson 12: The immortal genome

Personal decisions, moral quandaries, legal questions, and the future of genetics

Jason

 

[Simon Rose]

Hey everybody I've just taken the epigenetics course too, and now I'm doing the virology course. I'm also waiting for the tissue engineering course to start, if it ever does although I think it might be difficult to follow without actual hands-on lab work.The epigenetics course was mentioned in Nature recently as being an exemplary MOOC so I'm really pleased I did it. Although there seems to be much debate about the utility of MOOCs I think they might be the wave of the future what with rising tuition fees and so forth. I certainly learned a lot.

[Dakota Hamill]

Maybe teaching these courses locally is not such a bad idea...could charge 1/10th the tuition and still fund the experiments + pull a profit.  Do you know how many other people were in your "class"?

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[Cathal Garvey]

Yea, I think that's closer to the "future".

MOOCs, like "Open Access Journals", are a transitional phase of
top-down academic organisation towards a more distributed, "P2P"*
arrangement.

So, I imagine the real situation to expect is a wider web of
shared/reviewed course modules that local teams teach and share. Local
lecturers running from expert, peer-reviewed slides and notes with
open-access, regularly updated textbooks.

Strange really, that academic research which contributes to the body
of knowledge is expected to be peer reviewed and verified or falsified
by ongoing work, but the other end of academia is generally "special
sauce" kept close by tutors and hidden from scrutiny. I've seen plenty
of course material that's beyond flawed, it's downright pseudoscience;
lecturer opinion or speculation taught as fact.

But the pure top-down MOOC model, like the Open University (which
preceded this "MOOC" hipster reinvention), does lack in the direct
experience. For some academic branches, this might be OK; where
knowledge alone is imparted rather than a mix of knowledge and skill,
but for biology I think it's poorly suited.

..but then, that's why we recommend biohackerspaces for n00bs, right?
Go do, then ask?
-Cathal

*Given that academia requires expertise, and relative expertise creates
gradients of peerage, perhaps Academic "P2P" stands for "Privilege to
Populat"? :)

On Wed, 4 Sep 2013 18:24:30 -0400
Dakota Hamill <dko...@gmail.com> wrote:

> Maybe teaching these courses locally is not such a bad idea...could
> charge 1/10th the tuition and still fund the experiments + pull a
> profit. Do you know how many other people were in your "class"?
>
>
> On Wed, Sep 4, 2013 at 6:10 PM, Simon Rose
> <excalib...@googlemail.com>wrote:
>
> > Hey everybody I've just taken the epigenetics course too, and now
> > I'm doing the virology course. I'm also waiting for the tissue
> > engineering course to start, if it ever does although I think it
> > might be difficult to follow without actual hands-on lab work.The
> > epigenetics course was mentioned in Nature recently as being an
> > exemplary MOOC so I'm really pleased I did it. Although there seems
> > to be much debate about the utility of MOOCs I think they might be
> > the wave of the future what with rising tuition fees and so forth.
> > I certainly learned a lot.
> >
> > On Tuesday, July 23, 2013 7:15:23 PM UTC+1, Jason Bobe wrote:
> >>
> >> University of Guelph is offering a new online course: Introduction
> >> to DNA Barcoding:
> >>

> >> http://dnabarcodingcourses.**com/course-description/#.html<http://dnabarcodingcourses.com/course-description/#.html>

[Simon Rose]

Hi Cathal I can see your point that MOOCs are probably not well suited to biology where getting your hands "wet" really matters but more to math and computing. I do have access to our biohacklab downstairs, but the trouble is that I cannot practice what I have learned as it is far above the level of what we are currently capable of in our lab. Next week we're going to do our first miniprep which I would love to get some hands-on experience  of but it is still  a far cry from the stuff I'm learning in virology. There is a huge split between theory and practice with biology  MOOCs it seems. I was hoping to  use the hacklab as a kind of makeshift university to learn molecular biology but I'm not sure how far I can go down this route.

On Tuesday, July 23, 2013 7:15:23 PM UTC+1, Jason Bobe wrote: