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Joined: Fri Feb 29, 2008 5:26 am
Posts: 56
Post Links
I was thinking we could start a thread to share related links...

dnatube: A youtube for various biology videos

UCSF Chimera: I haven't seen this program before, but it's free molecular/protein simulation software (it runs on Windows, Mac OS X, and Linux).


Wed Mar 26, 2008 8:44 am
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Post Re: Links
Welcome back :)

I hadn´t seen the DNATube site, it looks very intresting. I added a bb code for the site.

---Edit: 2009-04-21. DNATube changed the way their videos are embedded. If you want to embed DNATube videos the new way to do it is like this:

In the bottom of the DNATube video window click the "Post to my social network or blog" icon.

You'll then get a link that ends with:

Code:
...f=http://www.dnatube.com/player/vConfig_embed.php?vkey=a242c43ad6590368912d" type="application/x-shockwave-flash" />   


The needed part is the vkey code. Underlined here.

...vkey=a242c43ad6590368912d"...

The key copied between the dnatube blocks like this...
Code:
[dnatube]a242c43ad6590368912d[/dnatube]
gives:



--- end edit

My contribution is the "Futures in Biotech" podcast.

We talked about it before but it belongs in this thread. Link is here

Also the Bayblab podcast can be very amusing. It's basically some students discussing biology and what comes to mind, sometimes drunk, often in terrible audio. It can be found here.

(...and heh, yeah :D ...Canadian)


Wed Mar 26, 2008 8:30 pm
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Post Re: Links
The OpenWetWare site is a given:
Quote:
OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering

Their homepage is www.openwetware.org

Associated to them is "The MIT Registry of Standard Biological Parts". It can be found here.

Check out the 'Browse Parts By Type' link from there, it puts a big smile on my face.

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Thu Mar 27, 2008 2:27 am
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Post Re: Links
"GEN, Genetic Engineering & biotechnology News" has a collection of short(10min) podcasts they call "GEN casts". They are mostly about medical biology. They are mady by General Electric, the company that builds the Borg Cubes. The link is www.genengnews.com/gencasts.aspx

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Sat Mar 29, 2008 1:30 am
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Post The Berkeley General Genetics Podcasts
The Berkeley General Genetics Podcasts

A Berkeley lecture series on Genetics, by a very animated man called Fyodor Urnov. Highly recommended:

Link is here.

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Sun Mar 30, 2008 1:58 pm
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Post Re: Links
CDC - Office of Health and Safety (Link)


Has various documents on Biosafety, waste removal, lab procedures, etc. (Biosafety in Microbiological and Biomedical Laboratories in particular stands out to me.)


Fri Apr 04, 2008 3:56 pm
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Post Re: Links
The Open Biohacking Project / Kit

Advertised as "This open, free synthetic biology kit contains all sorts of information from across the web on how to do it: how to extract and amplify DNA, cloning techniques, making DNA by what's known as oligonucleotides, and all sorts of other tutorials and documents on techniques in genetic engineering, tissue engineering, synbio (synthetic biology), stem cell research, SCNT, evolutionary engineering, bioinformatics, etc."

This is a collection of documents from the web. The 2008-01-08 version contains some errors. Like an OpenWetWare directory which is in a preformatted state for a content management system. I also had trouble unpacking the file with Winzip.

The collection, housed by sourceforge, can be found here.

The 18 year old authors homepage is here.

This is definitely biopunk.

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Mon Apr 07, 2008 9:09 am
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Joined: Mon Apr 07, 2008 12:29 pm
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Location: Austin, TX
Post Re: Links
Hey,

The link to dnatube is awesome. On that note, I have a few projects related to online video sites; the idea is that, ideally, we can go deploy some servers to keep track of videos related to our projects, while also providing a micropayment gateway. Check out an example over here. There's still a little work to be done, like making a public interface to add your own video links and so on, but otherwise it's finished. Last night I was emailing the guys behind Jove.com about adding this into their system.

As for the errors in the biohacking kit -- I am completely willing to fix the errors, and it's about time for an update anyway, I have tons of new files to add to the project. I am welcoming any of you to help me out and fix the errors. Patrik mentioned something about the filenames being too long. And there needs to be a way to convert the OWW wiki stuff into HTML.

While I am at it: yesterday (2008-04-06) Mackenzie and friends announced to some mailing lists (like the synthetic biology mailing list and the BBF mailing lists) the existence of diybio.org, the latest Boston biopunk group, mostly made up of people who have been competing in iGEM (which, btw, is looking for new teams- I've been arranging one at my local high school).

Hm. Does anybody have a mediawiki extension for dnatube?

- Bryan


Mon Apr 07, 2008 12:36 pm
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Post Re: Links
It's good to see you here ;)

/p


Tue Apr 08, 2008 3:41 pm
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Post Re: Links
kanzure, those were some good links.

I especially liked the diybio.org link. I'm definitely going to follow that group. It's good to see biopunk in action ;).

Can you tell me, is the diybio group affiliated with the university or is it separate? I never understood this.

again.. great links

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Thu Apr 10, 2008 10:50 am
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Post Molecular Neuropsychopharmacology streaming vids
From Wayne State University:

A semesters worth of streaming videocasts on Molecular Neuropsychopharmacology can be found here.

Thanks Kanzure

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Thu Apr 24, 2008 12:18 am
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Post Webcasts
Two Molecular biology Berkeley course webcasts

MCB 110 General Biochemistry and Molecular Biology

MCB 130 Cell Biology

These are simply wonderful lectures, highly recommended. The complete catalog of Berkeley online lectures is here. The lectures are undergraduate level(mostly) classroom lectures on topics like biology, chemistry, computer science, history and psychology. The catalog spans back to 2001.



National Institutes of Health webcasts

Hundreds of talks on medicine some of which enter into the field of molecular biology. The sizes of the videofiles are huge for some reason. Link is here.

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Sat May 17, 2008 5:43 pm
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Post Re: Links
MIT Audio/Video Courses

There seems to be less video content than in the Berkeley casts. Where Berkeley videocasts whole courses MIT seems to do that for some courses and only the introductory lectures on others. Link is here. Recommended.

Thanks Giovanni

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Sat May 24, 2008 3:06 pm
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Post Re: Links
Researchers Launch Online Protein Folding Game

Multiplayer online gaming brings to mind fabulously successful titles, such as "World of Warcraft" and "Ultima." On May 8, Howard Hughes Medical Institute (HHMI) researchers at the University of Washington are bringing the arcane world of protein folding to the online gaming arena with the launch of "Foldit," a free game in which players around the world compete to design proteins. The real world benefit: Scientists will test proteins designed by the game's players to see if they make viable candidate compounds for new drugs. . . .

Users can access the game via the web at http://www.fold.it/



Thanks Giovanni

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Sat May 31, 2008 7:46 am
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Post Re: Links
Pimm - Partial immortalization

This is just a blog, but it is well written and updated frequently.


Sun Jun 08, 2008 12:11 pm
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