Also, I just realized I've had over 25,000 hits on this blog. Thanks for reading! I hope it's been useful and interesting!NO on 37! Think about it, Californians. Are you telling me you can't figure this one out, @carighttoknow? #prop37 twitter.com/mjcgenetics/st…
— Michael James Clark (@mjcgenetics) November 6, 2012
genomics . bioinformatics . biotechnology . sequencing . opinions
Showing posts with label blogging. Show all posts
Showing posts with label blogging. Show all posts
Monday, November 5, 2012
Save the Square Watermelons
Thursday, November 1, 2012
"Why I Don’t Want to Know My Genome Sequence"
"Why I Don't Want to Know My Genome Sequence"
Kind of interesting to read this as someone who at least has his own exome sequenced and has learned a lot from it. It's kind of interesting to read it in contrast to my own post explaining why I wanted to sequence myself.
It ends with a funny statement:
To be more specific, let's use myself.
Sure, I could have lived my life thinking my borderline migranes were from caffeine withdrawel and my mother and not bothered to find out the exact mutations likely to cause it and therefore which drugs may actually have a beneficial effect on me. I could have. But I didn't.
I could have lived my life thinking my intestinal issues were due to a bad diet or food allergies. Because clearly copious amounts of salad, low fat, low carb, low salt is a bad diet, right? And clearly my wife who eats the same things and has zero gastrointestinal issues is just lucky. Oh no, it must be food allergies. It couldn't possibly be that I inherited two mutations, one from each parent, that damage a particular gene already known to be causative for gastrointestinal problems (among a number of other things that I happen to have that most general practitioners wouldn't link together).
I could have survived without knowing I have asthma. Maybe.
I mean, go ahead and live in ignorance if that's your thing. If you're not interested in your own genetics, then fair enough. You're not alone. But it was damn reassuring to me, personally, to figure out exactly what genes are mutated and how those are causing conditions that negatively effect me.
And I would say not only am I healthier, but I'm also more aware of my health. And that's a good thing.
And that genetic information isn't going to expire.
Anyway, let's not devalue our genetics this way. The fact that we don't know everything yet doesn't make the data itself less valuable. Yes, it will take effort to understand but then again, so does nearly everything about your health and life.
I see it as a great thing.
Kind of interesting to read this as someone who at least has his own exome sequenced and has learned a lot from it. It's kind of interesting to read it in contrast to my own post explaining why I wanted to sequence myself.
It ends with a funny statement:
An osteoarthritis mutation manifested itself as an inability to play an F chord at age 33. A p53 mutation and then another that bloomed in response to years of orthodontia X-rays gave me thyroid cancer a few years after I gave up the guitar. And I don’t need a genetic test to know I didn’t inherit my father and grandfather’s psychotic depression.
Ron Crystal, even though he’s among the sequenced, has the right idea: don’t smoke, exercise, eat a healthy diet, and don’t worry about DNA sequences. That’s good enough for me – at least for now.This is one of those statements used to make one's self feel better about not doing something he or she wants to do. That's my feeling, at least.
To be more specific, let's use myself.
Sure, I could have lived my life thinking my borderline migranes were from caffeine withdrawel and my mother and not bothered to find out the exact mutations likely to cause it and therefore which drugs may actually have a beneficial effect on me. I could have. But I didn't.
I could have lived my life thinking my intestinal issues were due to a bad diet or food allergies. Because clearly copious amounts of salad, low fat, low carb, low salt is a bad diet, right? And clearly my wife who eats the same things and has zero gastrointestinal issues is just lucky. Oh no, it must be food allergies. It couldn't possibly be that I inherited two mutations, one from each parent, that damage a particular gene already known to be causative for gastrointestinal problems (among a number of other things that I happen to have that most general practitioners wouldn't link together).
I could have survived without knowing I have asthma. Maybe.
I mean, go ahead and live in ignorance if that's your thing. If you're not interested in your own genetics, then fair enough. You're not alone. But it was damn reassuring to me, personally, to figure out exactly what genes are mutated and how those are causing conditions that negatively effect me.
And I would say not only am I healthier, but I'm also more aware of my health. And that's a good thing.
And that genetic information isn't going to expire.
Anyway, let's not devalue our genetics this way. The fact that we don't know everything yet doesn't make the data itself less valuable. Yes, it will take effort to understand but then again, so does nearly everything about your health and life.
I see it as a great thing.
Wednesday, November 16, 2011
Stop SOPA
I'm not a huge politics guy, so I don't want to go on a tirade about the Stop Online Piracy Act. Sufficed to say, it's a huge censorship bill parading as a bill to protect intellectual property. While I think the majority of us support protecting IP, I can't imagine the best way to do so is to monitor everything we do and censor websites based on some government-backed list of sensitive content.
As an example, if someone were to post copyrighted material in the comments section of my blog without my notice, my blog could potentially be shut down (censored) because of it. If I were to link to a site that had, somewhere on it, shared copyrighted material (even if I had no idea it was there and didn't intend for anyone to go there and see it or download it), my blog could be shut down (censored).
Moreover, the bill basically forces both providers and hosting services to strongly monitor content and shut down sites that potentially "infringe" on protected IP. Ever posted a picture of something that was copyrighted? Ever shared a link to a YouTube video with a copyrighted song in the background? That could be enough to get you shut down (because your host or provider doesn't want to be sued).
My wife and I often talk about the situation in Japan (she's Japanese) regarding the Fukushima nuclear reactor situation and how censorship and control of the media in Japan is so strong that the general public has no idea how dire the situation is. We even see that censorship and media control bleed over to here in America, where the general public is under the impression the nuclear situation isn't as bad as it is, in large part because the government and big media have an incentive to see nuclear power as an industry succeed.
Now here's the scary thing: If I were to start posting excerpts from copyrighted articles about that topic to respond to, if SOPA were to pass, my blog could potentially be shut down. I could personally be denied access. It's unclear to me exactly how much power this bill would give big media and the government. And that's the major problem.
In our field of genomics, a lot of us utilize freedom of sharing information and media to rapidly advance the science. I understand that this bill is meant to limit piracy of software and other digital media, but it represents a foot-in-the-door to all sorts of censorship. Could SEQanswers, for example, be sued for having a post up that contains the Illumina adaptor sequences? It certainly has been threatened in the past based on such things, but with SOPA passed, SEQanswers very well could have been shut down for that. What a detriment that would have been to the genomics and bioinformatics community.
Anyway, I just wanted to share this on my outlet to the world, as it is a very important issue generally and to our field in particular.
If you are an American and you do not support SOPA, please send a notice to your congresspeople telling them not to support it, either.
As an example, if someone were to post copyrighted material in the comments section of my blog without my notice, my blog could potentially be shut down (censored) because of it. If I were to link to a site that had, somewhere on it, shared copyrighted material (even if I had no idea it was there and didn't intend for anyone to go there and see it or download it), my blog could be shut down (censored).
Moreover, the bill basically forces both providers and hosting services to strongly monitor content and shut down sites that potentially "infringe" on protected IP. Ever posted a picture of something that was copyrighted? Ever shared a link to a YouTube video with a copyrighted song in the background? That could be enough to get you shut down (because your host or provider doesn't want to be sued).
My wife and I often talk about the situation in Japan (she's Japanese) regarding the Fukushima nuclear reactor situation and how censorship and control of the media in Japan is so strong that the general public has no idea how dire the situation is. We even see that censorship and media control bleed over to here in America, where the general public is under the impression the nuclear situation isn't as bad as it is, in large part because the government and big media have an incentive to see nuclear power as an industry succeed.
Now here's the scary thing: If I were to start posting excerpts from copyrighted articles about that topic to respond to, if SOPA were to pass, my blog could potentially be shut down. I could personally be denied access. It's unclear to me exactly how much power this bill would give big media and the government. And that's the major problem.
In our field of genomics, a lot of us utilize freedom of sharing information and media to rapidly advance the science. I understand that this bill is meant to limit piracy of software and other digital media, but it represents a foot-in-the-door to all sorts of censorship. Could SEQanswers, for example, be sued for having a post up that contains the Illumina adaptor sequences? It certainly has been threatened in the past based on such things, but with SOPA passed, SEQanswers very well could have been shut down for that. What a detriment that would have been to the genomics and bioinformatics community.
Anyway, I just wanted to share this on my outlet to the world, as it is a very important issue generally and to our field in particular.
If you are an American and you do not support SOPA, please send a notice to your congresspeople telling them not to support it, either.
Tuesday, October 4, 2011
And he's back with a site redesign!
You may have been wondering: Where have I been?
Choose from the following:
Answer:
If you checked any of the above boxes, you're correct! Congratulations.
Yes, it's been a very busy time in my life, but I am finally back and promise to update more often than ever before.
Also, I hope readers like the site redesign. This is a new offering from Blogger. A dynamic theme that allows you to choose how you'll view it from the dropdown menu on the left. I'm a big fan of the "Magazine" look, so that's what I've set to default.
Also, here's a cool site: [http://opensnp.org/] Basically, they let you sign up and will host your DTC SNP chip data with them free (with all the consequences* that comes with).
Finally, this offer from 23andMe is interesting. $999 for an 80x human exome. That's raw data only, folks. No analysis. I've got a long post about this whole thing in mind that I'll put up in the coming days. Still, it's a great opening salvo in the DTC/PGM era. Exome-seq DTC is truly here. Finally.
*Consequences unspecified. You should be protected by GINA regardless and, honestly, if someone wanted to know your genotypes so bad they could just pick up that coffee cup you threw away last week and do it themselves. But whatever, you still better ask dad before you post half of his DNA on the web.
Choose from the following:
Answer:
If you checked any of the above boxes, you're correct! Congratulations.
Yes, it's been a very busy time in my life, but I am finally back and promise to update more often than ever before.
Also, I hope readers like the site redesign. This is a new offering from Blogger. A dynamic theme that allows you to choose how you'll view it from the dropdown menu on the left. I'm a big fan of the "Magazine" look, so that's what I've set to default.
Also, here's a cool site: [http://opensnp.org/] Basically, they let you sign up and will host your DTC SNP chip data with them free (with all the consequences* that comes with).
Finally, this offer from 23andMe is interesting. $999 for an 80x human exome. That's raw data only, folks. No analysis. I've got a long post about this whole thing in mind that I'll put up in the coming days. Still, it's a great opening salvo in the DTC/PGM era. Exome-seq DTC is truly here. Finally.
*Consequences unspecified. You should be protected by GINA regardless and, honestly, if someone wanted to know your genotypes so bad they could just pick up that coffee cup you threw away last week and do it themselves. But whatever, you still better ask dad before you post half of his DNA on the web.
Wednesday, July 20, 2011
Mendel Google Doodle
Friday, July 1, 2011
Gists
I've been super busy writing a paper lately, so I apologize for the lack of updates. I do intend to comment on the recent 23andMe paper soon™.
A new feature on the blog is my Gist feed and a link to my Gist page. Gist is basically a quick-and-dirty code-sharing site from Github. Since I'm a quick-and-dirty bioinformatics programmer, I'll do my best to keep random code snippets that might have general application for others up there and publicly available. Also, please feel free to fork my code, fix it, et cetera.
My first Gist is an interesting one: A shell script for calculating mean heterozygous allele balance from a VCF4 file (basically GATK output with the "AB" INFO field). Very simplistic, but fast and easy to use for people wondering what the overall reference bias is in their variant calls.
A new feature on the blog is my Gist feed and a link to my Gist page. Gist is basically a quick-and-dirty code-sharing site from Github. Since I'm a quick-and-dirty bioinformatics programmer, I'll do my best to keep random code snippets that might have general application for others up there and publicly available. Also, please feel free to fork my code, fix it, et cetera.
My first Gist is an interesting one: A shell script for calculating mean heterozygous allele balance from a VCF4 file (basically GATK output with the "AB" INFO field). Very simplistic, but fast and easy to use for people wondering what the overall reference bias is in their variant calls.
Thursday, May 6, 2010
Google Verified Blogging
The next step in optimizing the Blog involves making sure it gets visibility through Google searching by getting it "Google Verified". This is really simple.
Go to Google Webmaster Central and sign in. Add your blog. Your blog will be added instantly, but you'll have to verify it. This is easy to do using the meta tag with Blogger. Go to your Blogger Dashboard, go to Layout, and edit HTML. Go to the bottom of your layout's head and insert the meta tag. The easiest way to do this without screwing anything up is to put it right above the last line of the header. Voila! Verify your site after implementing the meta tag and you're good to go.
Google Webmaster Central includes some interesting stats especially regarding searches that pop up your blog. It's no replacement for GoogleAnalytics, but it does make it easier for Google to put your blog entries up as search results when appropriate.
Go to Google Webmaster Central and sign in. Add your blog. Your blog will be added instantly, but you'll have to verify it. This is easy to do using the meta tag with Blogger. Go to your Blogger Dashboard, go to Layout, and edit HTML. Go to the bottom of your layout's head and insert the meta tag. The easiest way to do this without screwing anything up is to put it right above the last line of the header. Voila! Verify your site after implementing the meta tag and you're good to go.
Google Webmaster Central includes some interesting stats especially regarding searches that pop up your blog. It's no replacement for GoogleAnalytics, but it does make it easier for Google to put your blog entries up as search results when appropriate.
Setting up GoogleAnalytics with Blogger
GoogleAnalytics is a very cool free online tool for tracking site usage and access. It includes some very cool features like showing usage over time, tracking sources and showing where users are viewing your page from. It's very simple to set up in a traditional webpage, too, by just planting a little snippet of code at the bottom of your pages. It's also very easy to set up on a Blogger page.
First, log on to GoogleAnalytics and set up a new account for your blog. You'll receive tracking code that needs to be inserted into the HTML of your blog's pages. Fortunately, this is really easy thanks to Blogger using a HTML template for every page of your blog.
In your Blogger Dashboard, go to Layout and add a gadget to the Footer. The gadget you want is "HTML/JavaScript". Now just copy and paste the tracking code from GoogleAnalytics into this gadget. (Leave the title blank--there's no need for it to have a title.) Save your layout and you should be good to go. Within a few hours, your GoogleAnalytics for your blog ought to have a green checkmark signifying that GA is receiving data from your blog.
For those with HTML savvy or heavily modified layouts, you can do the same thing by just putting the tracking code at the bottom of your page's body. Then again, you probably already knew that.
First, log on to GoogleAnalytics and set up a new account for your blog. You'll receive tracking code that needs to be inserted into the HTML of your blog's pages. Fortunately, this is really easy thanks to Blogger using a HTML template for every page of your blog.
In your Blogger Dashboard, go to Layout and add a gadget to the Footer. The gadget you want is "HTML/JavaScript". Now just copy and paste the tracking code from GoogleAnalytics into this gadget. (Leave the title blank--there's no need for it to have a title.) Save your layout and you should be good to go. Within a few hours, your GoogleAnalytics for your blog ought to have a green checkmark signifying that GA is receiving data from your blog.
For those with HTML savvy or heavily modified layouts, you can do the same thing by just putting the tracking code at the bottom of your page's body. Then again, you probably already knew that.
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