Category Archives: Tech, Tools, Toys

Anonymous Social Media Overview, Part Three: The Whisper Controversy & Beyond

I had said in Part Two of this series that I was waiting to talk about the Whisper Controversy because it was still unfolding so dramatically. Things are starting to wind down, and so last night I put together a Storify mapping out my perspective of the timeline of how this has all been happening.

Briefly, Whisper was trying to do a good thing, but it seemed to go wrong.
Guardian called them out on issues related to privacy & user tracking.
Story exploded.
Whisper defended themselves (mostly via Editor-in-Chief).
More explosions.
Guardian gleefully expanded on their original story.
Yada yada.
Whisper tries to regain trust (mostly via CEO).
Editorial team “laid off” pending investigation.
And now the clean up work starts.

Check the Storify for more details and specifics.

Meanwhile, Whisper is not alone. Far from it! Snapchat was hacked. Snapchat is probably the most famous anonymous social media app right now. Before they were hacked, all sorts of people were making tools (1, 2, 3) to “break” Snapchat’s rules about keeping copies of deleted pictures without permission. (The same sort of thing is happening on other ‘anonymous’ social platforms, like Tumblr with KnowAnon. And people posted private sex tapes on YikYak, which is also infamous for cyberbullying and violence and threats.) And the Federal Trade Commission is investigating some of the problems with Snapchat. People still trust and use Snapchat. And there are apps designed explicitly to, well, invade your privacy on an opt-in basis, like PeekInToo. This post has focused on the privacy issues, but violence, dishonesty, and cyberbullying remain significant issues in many online spaces. So, that’s the bad news. In the next post, I’ll look at some of the good things being done with social media.

Anonymous Social Media Overview, Part One: Context, Risks, Benefits & Opportunities, Best Practices

CONTEXT

Following on the heels of Monday’s post about suicide prevention as it intersects with anonymous social media, I thought it might be helpful to have an overview of some anonymous social media apps, and the current state of the conversation around their risks and benefits. One of the reasons this seems to keep coming up is the NYMWARS (or, as Danah Boyd puts it, The politics of “real names”). While this issue arose originally in 2011, it never seems to really go away. Today’s Twitter feed for the hashtag #nymwars gives evidence of this.

There is a lot more where that came from. Danah described the issue as being one of power and control.

“When people are expected to lead with their names, their power to control a social situation is undermined. Power shifts. The observer, armed with a search engine and identifiable information, has greater control over the social situation than the person presenting information about themselves. The loss of control is precisely why such situations feel so public. Yet, ironically, the sites that promise privacy and control are often those that demand users to reveal their names.” Comm ACM 2012 55(8):29-31.

There are many who believe that requiring transparency (as in ‘real name’, as in the name on your birth certificate) of all users helps to protect the community from bullying and rudeness and other uncivil behavior. This is debatable, and there is supporting evidence on both sides of the debate. At the same time, forced transparency endangers others in the community (anyone at risk or in a marginalized population) at the same time it undermines identifying anyone who uses a pseudonym as their primary identity.

Facebook is enforcing its “real names” policy, insidiously outing a disproportionate number of gay, trans and adult performers — placing them at risk for attacks, stalking, privacy violations and more. Facebook is strong-arming LGBT and adult performers to use their legal names, telling these at-risk populations that it is to “keep our community safe.” Facebook nymwars: Disproportionately outing LGBT performers, users furious

While there is an acknowledged emphasis in the current fuss over Facebook names on excluding LGBT persons, the problem is much broader, and also effects many people with unusual real names. Chase Nahooikaikakeolamauloaokalani Silva is one recent example, but it is so common that Facebook has a section of their help site devoted to these incidents.

"Facebook says my name is fake. It is real."
Facebook says my name is fake. It is real. https://www.facebook.com/help/community/question/?id=10151790248568209

Unfortunately, when this happens to people, Facebook will only consider correcting the problem when supplied with a copy of a legal government ID, such as a passport, drivers license, or birth certificate. Sometimes, those aren’t good enough, which REALLY annoys people. If it was me, I would not be happy or feel safe supplying a copy of my government ID to Facebook or via electronic means. That entire approach is not only an invasion of privacy, but a strategy that would seem to place the victim at risk of identity theft. It just makes me really nervous. When this arose back in 2011, the Electronic Frontier Foundation distilled the concept of NYMWARS as an important trend for that year.

EFF immediately advocated for the right of users to choose their own names on social networking sites, whether they’re women or minorities concerned about their privacy, activists in authoritarian regimes who want to speak out without the threat of government harassment, or users with persistent nicknames or pseudonyms they’d used online for years…. EFF had been loudly opposed to Facebook’s “real names” policy for years, pointing out that community policing of real names silences some of the people who need this protection the most—people with unpopular opinions—because opponents can easily have their accounts suspended by reporting them as pseudonymous. 2011 in Review: Nymwars.

My favorite piece, and the best short distillation I’ve seen was posted to Facebook a little over a week ago by one of my favorite people in healthcare social media, @DrSnit. It is substantially excerpted here with permission.

Requiring a “legal name” is problematic for the following: 1) counselors and therapists avoiding a stalking client 2) physicians avoiding patients seeking medical advice 3) Attorneys dealing with angry criminals with a vendetta 4) women (like me) dealing with abusive partners & leaving abusive relationships. Those people who are being stalked or have been stalked WHO DO NOT WISH TO BE FOUND BY THEIR EX’S OR EX’S FAMILY & FRIENDS 5) Gender queer people, butch lesbians, and trans people who use different names than the names they were given at birth. 6) Stage performers, writers, artists who use different names for their art and their family / friends 7) People who use their middle names or nick names from birth or derivatives from birth. (This is off the top of my head – not exhaustive list).

Legal names are good for: stalkers, abusers, ADVERTISERS

FB claims it is to keep stalkers and abusers from taking fake names to harm people – but stalkers are REALLY GOOD at what they do and use nefarious methods to deal their damage. FB isn’t protecting anyone. They are harming people who CHOOSE to use different names because because it messes with their advertising analytics. Don’t let them. You don’t NEED FB bad enough to be harmed by their policy. If anyone you know has been hurt or stalked – let FB know and if they don’t change their policy – use other social media that is more women and safety friendly.

Let me repeat the most important line.

Legal names are good for: stalkers, abusers, ADVERTISERS

So, with that as context, perhaps the explosion of anonymous social networks may be, at least in part, a reaction to the forced transparency of other social networks. I have friends who have always used a “fake” name on Facebook. It is their real identity, and it sounds and looks like a normal name, and Facebook has never given them any trouble about it. I also know of those who are using their legal name, and getting hassled about it. The upshot is that anonymous networks are a justifiable response, but they carry their own risks, and their own benefits. Let’s take a quick look at some of these.

RISKS

There are a lot of nasty words tossed around about the bad side of anonymous online services. The big ones seem to be that (1) they are not really anonymous; (2) people are mean (bullying & more); (3) you can be victimized in many different ways. Here are some of the types of words used in articles that describe the risks of anonymous social media and social networks.

abuse
bullying
character assassination
hacking
harassment
identifiability
falsehoods
lies
not anonymous
prejudice
racism
rape
sexism
sexting
sexual predators
solicitation
stalking

BENEFITS / OPPORTUNITIES

Safe spaces for persons who need anonymity to be safe or to be treated equitably, such as
– Battered wives,
– Persons who are part of a marginalized or abused community,
– Celebrities,
– Whistleblowers,
– Political minorities,
– Political dissidents,
– Crime witnesses.

Suicide prevention & outreach.

Crime prevention

Therapeutic benefits of engaging for those with social anxiety.

Reaching out to those who suffer from shame.

Free speech on unpopular issues without fear of reprisal

Domestic violence support groups or outreach

Advice channels / threads / tags

Therapeutic channels / threads / tags

BEST PRACTICES FOR ENGAGING (MAYBE)

Don’t ask / Don’t tell (personal information).

Don’t identify yourself.

Don’t use your name.

Don’t use a known pseudonym.

Don’t use a friend’s name.

Don’t ask others to identify themselves.

Don’t describe your location, appearance, or other identifiable characteristics.

Don’t give your email address, street address, phone number, or other direct contact information.

Ask others you trust if they’ve had good or bad experiences there.

Post harmless stuff while testing.

TEST IT OUT!!

MORE SOURCES

(1995) Rigby, Karina. Anonymity on the Internet Must be Protected. http://groups.csail.mit.edu/mac/classes/6.805/student-papers/fall95-papers/rigby-anonymity.html

(2002) Dvorjak, John C. Pros and cons of anonymity. http://www.pcmag.com/article2/0,2817,801688,00.asp

(2011) Bayley, Alex Skud. Preliminary results of my survey of suspended Google+ accounts. http://infotrope.net/2011/07/25/preliminary-results-of-my-survey-of-suspended-google-accounts/

(2011) McElroy, Wendy. In Defense of Internet Anonymity. http://mises.org/daily/5541/

(2011-2014) Geek Feminism Wiki. Who is harmed by a “Real Names” policy? http://geekfeminism.wikia.com/wiki/Who_is_harmed_by_a_”Real_Names”_policy

(2013) Santana, Arthur D. Virtuous or Vitriolic: The effect of anonymity on civility in online newspaper reader comment boards. http://www.tandfonline.com/doi/abs/10.1080/17512786.2013.813194

Common Problems in Systematic Review Searches: Right Side Truncation? NOT! (A PreziTube Test)


Common Problems in Systematic Review Searches: Right Side Truncation? NOT! https://www.youtube.com/watch?v=WMLiozo-lwg

A couple days ago, I was offered a coupon / voucher to test PreziTube. PreziTube is a tool that automatically exports your Prezi presentation to a Youtube video format, both downloadable and with the option of automatically uploading to Youtube. For this test, the automatic upload option ended up in their Youtube account, not mine, and I am not sure if there is an option to work around that if you pay for the privilege.

Playing with Prezitube & iMovie
PreziTube: http://prezitube.com/

Now, I’ve had issues for a LOOOONG time with the lack of accessibility in Prezi. This seemed like a tool that might help with some portion of that process, so I was interested. Definitely interested.

I went to Prezi to find whichever of my Prezi presentations is the most popular. Ah, yes, one on systematic review searching and truncation.

Systematic Review Searching: Right-Side Truncation? NOT! http://prezi.com/77qy3sfhq_tv/systematic-review-searching-right-side-truncation-not/

I put in the link and the voucher code and gave it a try.

Playing with Prezitube & iMovie

Prezitube offers a variety of timing options, but the assumption is that each “slide” within the Prezi will receive the same length of time. Since this presentation was rather text heavy, and I wasn’t sure just how long these times, I went for the middle. The range offered is from 4 to 30, and for this video I chose 15.

I downloaded the video, wished I had an audio voiceover, but didn’t want to take the time, so I just grabbed some amusing-to-me public domain audio from the Internet Archive, and spliced that in with iMovie. I have access to other video editing tools, but I wanted to see what could be done with virtually no resources.

Playing with Prezitube & iMovie

And the link to the audio track used.

Kay Kyser – Some Day I’ll Find You 1937 (posted as “Kay Kaiser&kollegeOf MusicalKnowkege10f2″) https://archive.org/details/KayKaiserkollegeofMusicalknowkege10f2

Now, this took almost no time at all. It probably took me about a half hour to make the video. It took me about 2 hours to upload it to Youtube, because Youtube was being glitchy that day. Not great, but absolutely worth a half hour of my time.

Now, do I want to do this for more Prezis? The free version gives you tiny videos and you can’t download. For $6.99 you may download and get high resolution videos, with support if something goes wrong. Hmmm, maybe, maybe. Maybe next time, I’ll do the systematic review Prezi on phrase searching.

Systematic Review Searching: Word Order in Phrase Searching http://prezi.com/vrzaimpaignp/systematic-review-searching-word-order-in-phrase-searching/

Infographic of the Week: HHS Infographics Collection!

HHS Infographics on Flickr
Flickr: Group: HHS Infographics: https://www.flickr.com/groups/hhsinfographics/

I just discovered a Flickr group that collects infographics from the US Department of Health and Human Services. WOW. Talk about a great resource! There are many infographics in the collection, and also marketing images for specific health challenges or initiatives.

HHS Infographics on Flickr

This isn’t all they have, though! You can many of these in sets or albums from the HHSgov Flickr Stream.

Flickr: HHS: Sets: Health Care Infographics: https://www.flickr.com/photos/hhsgov/sets/72157633968047018/

Flickr: HHS: Sets: HHS Infographics: https://www.flickr.com/photos/hhsgov/sets/72157632180365890/

Now, it is completely wonderful to have a one stop shop to go hunt health infographics from a reliable source and of known high quality. Extremely useful! But this is even better than that. Because these are in a Flickr Group, there are many other things you can do.

If you have a Flickr account, you can request to join to track the images that appear in the group, or you can use the RSS feed from the group in your feed reader.

You could set up a computer display in a public area, and start the “slideshow” view from the group as a way to engage the public around quality health information.

Because these are licensed as “United States government work,” you can download these, re-use them, post them yourself, put them on your website, edit and modify them. As they say:

Anyone may, without restriction under U.S. copyright laws:
* reproduce the work in print or digital form;
* create derivative works;
* perform the work publicly;
* display the work;
* distribute copies or digitally transfer the work to the public by sale or other transfer of ownership, or by rental, lease, or lending.

Niiiiiice.

However, because these are in Flickr, the absolute easiest way to share them is to just embed them on your webpage or site, or share the link wherever you wish. Here’s an example.

Recently, I’ve been seeing many conversations on social media, on Twitter, Facebook, and in blogs, about issues with patients access to their electronic health record and problems with the accuracy of the information in their record. Right now, this is again a timely issue. The HHS has a series of four short infographics on exactly this topic. I can choose one or any or all and, with a Flickr account, grab the embed code to put them in this blogpost without having to download or upload or rename or identify or worry about the accessibility of the code. Here’s what it looks like.

Know Your HIPAA Rights #1Know Your HIPAA Rights #2
Know Your HIPAA Rights #3Know Your HIPAA Rights #4

If someone clicks on any of the four images above, it will take them to the original image, in a larger size. The source is right there, and I didn’t have to do the work. So very helpful. I love this resource. So glad I found them!

Infographic of the Week: 8 Early Warning Signs of Domestic Violence

Beauty Cares: #1 of 8 warning signs in nine languages
Beauty Cares: 8 Warning Signs of Domestic Violence: http://beautycares.org/signsofdomesticviolence/

I was extremely impressed when I discovered the Beauty Cares: Education = Prevention Tour on the topic of domestic violence. They have a wonderful infographic that spells out eight of the most common indicators forewarning of a relationship that is more likely to become a battering relationship in the future.

There are so many things I like about this it is hard to choose where to start. I like the information, and the design. I like that they say, “DOWNLOAD AND SHARE!” at the bottom of all the graphics. I like that they translated it into so many languages (some of which you see in the picture at the top of this post).

But what I like most is how they are using this in schools. When I first saw this my first thought was, “I wish they had a full course curriculum in every high school where this image was the syllabus!” Well, they aren’t taking this that far, but they are taking it into the schools as part of a formal outreach program. I found blogposts on recent visits to four schools (with many more in the blog archive): Mary Louis Academy; Cathedral High; St. Joseph’s; & Long Island University.

Just imagine a room where a teen girl tells a story about a recent date, and other teens erupt at one point in the story, “Unhunh, girl, that’s CONTROL. He’s trying to make all your decisions. What do YOU want?” Where all the teens know these and recognize them when they see them, and get conversations going around them. It could be so powerful.

I’ve showed this to a few married couples, too. Happily married couples. It seems (in my experience) as if it is pretty normal to have a couple of these show up in a healthy relationship, every now and then, and not at extreme levels. Still, they are there. So don’t go feel like you must leave a relationship immediately if you see one of these. But if you see several of them, or any one of them is WAY over the top and out-of-control, or it doesn’t come and go but is there ALL the time … well, you might have a problem. Also, think about what are YOU doing in your relationships? How many of these do your partner have to put up with? Feeling sheepish? Well, we’re only human. But do try to be aware, and try to get it under control. If you can’t do it yourself, get help. And if your partner can’t get it under control, get help, and get out. Even if getting out is just until they do learn how to control themselves better.

But there are folk who can say it better than I can, and who know a lot more about it than I do. Here is a video from the Beauty Cares channel, followed by the complete infographic. (You were wondering what the other seven signs are, weren’t you?)


Aryn Quinn: Preventing Domestic Abuse & Teen Dating Violence https://www.youtube.com/watch?v=VZLBj2opJP8

PDF: http://beautycares.org/wp-content/uploads/2012/12/SHARE-THE-8_-21-years-and-up.pdf

Beauty Cares: 8 warning signs of domestic violence

Beauty Cares: 8 Early Warning Signs of Domestic Violence:
1. Intensity
2. Jealousy
3. Control
4. Isolation
5. Criticism
6. Sabotage
7. Blame
8. Anger

Good Lord, People, 23andMe is NOT Dead!

Reposting from my personal genomics blog because I think it is important also for the audience of this blog.


23andMe

Good Lord, people, 23andMe is NOT dead! Or closed, or no longer taking orders, or anything like that. I hear this a lot.

“You know, I always wanted to get my genome tested. I was going to try 23andMe, but then the FDA shut them down. Oh, well, missed my chance. [sigh]“

NO! You did NOT miss your chance. Firstly, 23andMe is not closed for business. They still will take your money and your sample. They still will analyze the sample and give you results. From what I’ve been seeing in the results from folk I’ve been helping to look at their data, 23andMe seems to be running the test exactly the same way they always did, for the same SNPs.

They simply are, at this time, not offering their health reports to new customers. It isn’t the data that has changed – it iw what analysis is shared with the customer. Old fogies like me who got their tests done before the FDA folderol” still have access to our old 23andMe health reports, and they continue to improve them.

I have heard nothing to indicate that 23andMe are not working with the FDA to try to make it possible to release health reports again in the future. Issues around that get complicated and I’m going to save them for a later post. Right now, what if you wanted a test for some genetic health information? Can you do it? How long will you have to wait to find out the answers to your health questions?

You can still do it. It isn’t as easy as it was before, but it can be done. I’ve been spending a lot of time talking people through how to do this, and it is time to write it down. If nothing else, it will save me time. This will be the short short version, and I can answer more detailed questions and describe specifics, maybe give an example or two or three.

FIRST, THE DISCLAIMER

Risk is Not Just Genes

Making sense of genetic information is complicated even for experts, which most of us are not. Of course, part of the irony of looking at genetics for health conditions is that most of the time what causes the condition is not just the genetics, but genes PLUS something else. If you don’t find the genes for something, that doesn’t mean you can’t get it; if you do find the genes for something, it doesn’t mean you will get it. It is hardly ever a case of this=that.

What Does Risk Mean, Anyway?

There is also the challenge of figuring out how important the risk is, and whether or not to do something about it. So, my personal risk of celiac disease is over 4 times normal. Wow! That sounds like a lot, doesn’t it? But 4 times normal for celiac risk is still only 1 in 20 people, because normal is about 1 in a hundred. I know someone with celiac risk 17 times normal, which is 1 in 4 people. That’s getting to be pretty serious! But, while celiac is dangerous, it isn’t one of those conditions that is immediately deadly or painful. And my friend still has a 3 in 4 chance of NOT getting celiac, and that is a lifetime risk.

On the other hand, my risk of venous thromboembolism (VTE) is 1.5 times normal. That doesn’t sound like much does it? It’s higher, but only a little bit. So we don’t really need to worry about it, do we? Well, yes. VTE can kill you on the spot, and it is incredibly painful. And normal is 1 in 10 people for lifetime risk. For me, the risk is closer to 1 in 7.

Given that, according to 23andMe, my genetic risk of celiac is roughly 1/20 and my risk of VTE is 1/7, and adding in the comparative dangers of the two diseases, my docs got all excited about the VTE, and not terribly about the celiac. I hope you understand why now, and also a bit more about why genetic risk is complicated.

On Asking for Help

Last part of the disclaimer.

For both of these, celiac and VTE, 23andMe looks at SOME of the genes and SNPs known to be associated with the condition, but not ALL of them. So whatever 23andMe tells me about risk is only part of the picture. It looks at the most important genes, but is still only part of the picture. That’s why you need experts to put all the pieces together, and get more information to fill in the gaps from the 23andMe test.

Everyone always says, “Ask your doctor,” when it comes to finding something puzzling, confusing, contradictory, or worrisome in your genetic tests. I did, and found that most of my doctors didn’t have the expertise to make more out of it than I did. Some poohpoohed the 23andMe results, others made clinical decisions based on them without verifying with other tests, some asked for more medical tests to expand upon what 23andMe had, and one said, “You know more about this than I do, but I’m going to learn.” Here is a quote from an NEJM article a few months ago about the risks and benefits of trusting direct-to-consumer personal genomic services such as 23andMe.

“Clinicians will be central to helping consumer–patients use genomic information to make health decisions. Any regulatory regime must recognize this reality by doing more than simply adding the tagline on most consumer ads for prescription drugs: “Ask your physician.” That is insufficient guidance unless your physician has ready access to a clinical geneticist or genetic counselor.” Annas GJ, Elias S. 23andMe and the FDA. N Engl J Med 2014; 370:985-988. http://www.nejm.org/doi/full/10.1056/NEJMp1316367

Some of the personal genomics service offer phone-in access to genetic counselors. I tried that, and didn’t get helpful answers there, either. Even worse, one of the answers I got was blatantly wrong. It may have been just the genetic counselor who I happened to be talking with, so don’t judge the whole profession by that one person, but do be prepared to keep looking for info if needed. Where I found the most helpful information was in the 23andMe forums, BUT a lot of the info there was unreliable, and I had to sort out what was helpful and what wasn’t.

So, my recommendation is, absolutely DO ask your doctor, ask a genetic counselor if you can, but that might not be enough. You might need to do more research on your own, or find someone you trust to help you with this.

What Good Is It?

So, what good is it then? It gives you clues. Like a detective, you take the clues and look for more information, or ask for more thorough testing, or raise questions that weren’t being asked or addressed before. Some of the clues will be red herrings. Some of them may lead you to a prized solution. For me, these clues ended up dramatically improving my quality of life, and may have even saved my life.


So, now, the short short version. And PLEASE, if someone more expert than me with genomic data reads this and spots any errors, please say so!

PART ONE

1. Get your 23andMe test done.

Pic of the Day - PGenPGEN, Take 2

2. Log in at the 23andMe web site when you are notified that your results are ready.

23andMe

3. Click: Browse raw data.
23andMe: Getting to your raw data

It should look like this:

23andMe: Browse Raw Data

4. Click: Download raw data.
23andMe: Download Raw Data

5. Complete security procedure (log in again, answer security questions, etc.). It should look like this.

23andMe: Downloading Raw Data

6. Answer the question about what type of data and format you want. NOTE: I always choose ALL DNA, unless you have something else specifically in mind.

23andMe: Downloading ALL Your Raw Data Or ...

7. Find the file (which will be named something like genome_Firstname_Lastname_Full_12345678901234.txt)

PART TWO (A): Easier Way

Genetic Genie

Now you have choices. You can dig into the information the easier way, or the less easy way. Let’s start with the easier way.

1. Select a tool to do what you want with your data. There are LOTS of tools people have built to do useful things with 23andMe data files. One of my favorites is Genetic Genie, because it tells you about the MTHFR gene which has become so important in my life. I also am spending a lot of time with Promethease because it is so complete compared to most other 23andMe analysis tools. Lets start with these.

2. Go to the tool of your choice, such as:

Genetic Genie: http://geneticgenie.org/

Promethease: http://www.snpedia.com/index.php/Promethease

3. Follow the directions at the tool, but this almost always requires you to upload your 23andMe data file. Here are more details about doing this with Genetic Genie.

4. Last come what is always the tricky part — making sense of the information you get. That’s worth several posts, but for starters the main point to remember is that the 23andMe test is a place to start, not a final answer. In Genetic Genie, the code, analysis, and text are written by engaged amateurs, not by doctors or genetic counselors. They worked hard, collaborated with a lot of other people, and did a lot of research, but it isn’t going to say the same things your doctor might.

More Tools

23andMe: Tools for Everyone http://www.23andyou.com/3rdparty
NOTE: When 23andMe took out the health reports, they also edited this page to remove links to tools that provide health data from 23andMe data. So, this is interesting and useful, but not sufficient. You’ll have to look somewhere else for most tools.

23++ Chrome Extension: Get more from your data:
http://23pp.david-web.co.uk/getting-more-from-your-data/

Confessions of a Cryokid: Top 10 things to do with your FTDNA raw data (2011) http://cryokidconfessions.blogspot.com/2011/06/top-10-things-to-do-with-your-ftdna-raw.html

Genetic Genealogist: What Else Can I Do With My DNA Results: http://www.thegeneticgenealogist.com/2013/09/22/what-else-can-i-do-with-my-dna-test-results/

International Society of Genetic Genealogy: Autosomal DNA Tools: http://www.isogg.org/wiki/Autosomal_DNA_tools

Resqua: Q: What should I do after generating my Gene variance report? http://resqua.com/100005927200207/what-should-i-do-after-generating-my-gene-variance-report

Think Exponential: Get SNPd! http://thinkexponential.com/2013/01/10/why-you-should-get-snped/

PART TWO (B): Less Easy Way

Linking Disease Associations with Regulatory Information in the Human Genome

Actually, there are a LOT of different “less easy ways.” You can open the raw data file in a text editor and search manually for specific pieces of information. Or, if you code, you can write a little program to do some of the hard work for you.

Basically, it comes down to doing a lot of research, the hard way, by hand. But, believe it or not, I am doing it. I’ve had a lot of help from people who offered tips or comments in the 23andMe or MTHFR.net forums, on Facebook, on Twitter, and comments on these blogs. I am NOT an expert, but like most readers of this blog, just someone who wants or needs to know more. This is what I’ve learned and figured out on my own, offered as an example, nothing more.

Critical Background

23andMe gives SNP-based data. SNP stands for single nucleotide polymorphism. Polymorphism means something that can be itself but in different ways, our eyes are eyes whether they are blue or brown or hazel or violet or any other natural eye color. I won’t give an introduction to genetics here, but there are several online resources that explain these ideas, with one of the best resources being Genetic Home Reference from the US government. Depending on how much you want to know, you may wish to take the Coursera courses Introduction to Genetics and Evolution (Duke U) or Experimental Genome Science (U Penn).

1. What SNPs do you want to know about? Check here:

RegulomeDB (Stanford): Linking Disease Associations with Regulatory Information in the Human Genome: http://regulomedb.org/GWAS/

I have also found SNPs of interest in research articles, PUBMED, and other places, but this is a good start. The SNP identifier (what you need) will look something like this:

rs2187668

2. Find out which polymorphism is the one considered “healthy” or “normal”, and which one is the one associated with risk of disease? These maybe called “risk alleles” or
simply polymorphisms.

For example, for SNP “rs2187668″ (one of the celiac risk SNPs) the risk indicator is (T), while the normal is (C).

3. Open your 23andMe raw data file in a text editor, like WordPad (Windows) or TextEdit or TextWrangler (Macintosh).

4. Search for the SNP you want to know about. The data will be in four columns:
– RSID
– Chromosome
– Position
– Genotype
You need to know about the first and last columns, RSID and Genotype. It will look a little like this.

rsid…..chromosome…..position…..genotype
… [many other rows of data] …
rs2187668…..6………32605884…..CT

So, this person (me) has for that SNP one risk allele “T,” (which I happen to know is from my dad, by comparing it to his scan) and one normal allele “C,” (which must, by default, be from my mom, since for every gene pair we have gotten one from each parent).

5. Repeat for all the other SNPs associated with the condition you are researching.

6. Search for more information and articles about those SNPs, the condition, and more. You can’t make sense of this without more information. And ask lots of questions.

More Tools

ENCODE:
About: http://www.genome.gov/encode/
Data: http://genome.ucsc.edu/encode/

ENSEMBL Genome Browser: http://useast.ensembl.org/

OpenSNP: https://opensnp.org/ OR https://opensnp.org/snps/

SNPedia: http://www.snpedia.com/

UCSC Genome Browser: http://genome.ucsc.edu/

[#makehealth] Connecting Making (Hacking, Tinkering) to Health

GO-Tech Meeting at Maker WorksAnn Arbor Mini Maker Faire 2014Detroit Maker Faire 2013

So, you’re a Maker, Hacker, Tinkerer, Inventor, DIYer, Code Monkey, or all around Geek, and you think this #MakeHealth Fest sounds interesting and fun. You’re thinking of getting involved, BUT … (and it’s a big “but”) you’re not doing anything exactly, well, health-ish, not that you can think of, anyway. That’s why I’m writing this — just to show how some of these ‘traditional’ maker activities can connect to health projects, can help real people, if you want, in accessible real world ways. I wish I’d had time to make this into a lot of smaller posts, but we’re sending out the #makehealth call for participation next week, and I want all of you to think about how you could be involved or what you’d like to see when you come. You are coming, of course. ;)


3D printing

3d printer printing

I talk about 3d printing a lot. You know, Robohand, Project Daniel, babies with new tracheas, men with new faces, and more. But those are the exceptional examples that make the news. There are so many ways in which 3D printing is helping in more mundane ways. I had a shoulder and wrist injury and was having trouble opening jars. I found I could 3D print a jar lid gripper. Engineering students and physical therapy students at University of Detroit Mercy collaborated on designing better spoons (which they 3D printed). People are using 3D printing to repair broken equipment, make equipment clips to hold wires out of the road, practical things like that. Healthcare students have been using 3d printing to modify or adapt their stethoscopes. There are so many possibilities. It doesn’t have to be earth shattering to be a useful skill.


Arduino Uno, Beaglebone & Raspberry Pi

Raspberry pi

Arduino Uno, Beaglebone, and Raspberry Pi are inexpensive computing hardware, often used as controllers (microcontrollers) to get other equipment or objects to do something you want. They are incredible for assistive technologies! Something a person wants to do, perhaps used to do, but which is hard for them to do — is there a way you could design an inexpensive object to help them do it? Maybe remote control lights, sound, monitors? Connect them with sensors or trackers to do something when the input reaches a particular level.

How does this connect with health? Many ways. Firstly, most maker techniques and tools can be used as assistive technologies. Try searching any of these with the word(s) assistive or “assistive tech” or “assistive technology”, and you will find a flood of applications.

Google Search: (“Arduino Uno” OR Beaglebone OR “Raspberry Pi”) assistive

Secondly, connecting this to sensors automatically makes possible a wealth of applications in the area of the Quantified Self movement – tracking data about your self and/or home or environment with a goal of promoting and achieving personal health goals. These have been used for personal cardiac monitoring, tracking ECG and pulse rate, blood pressure; it can be used for other types of sensors — GPS, saline levels, alcohol levels, whatever sensors you have; to create a home sleep lab; managing data from mobile phone apps or GPS, such as exercise and calorie expenditure for weight loss; taking prescription meds on time; and much more. These are such inexpensive tools that they really lower the barrier to entry for many folk to get engaged in more hands-on tracking and management to match their personal goals.


Coding & Code-a-thon, Hackerspace & Hackathon

ImageJ Code Sample

The hardware isn’t much use without code to tell it what to do, so these seem like obvious connections. Everything mentioned in the prior section apply here. Because coding need not be device specific, these can have broader impact, tying in to larger computers, mobile devices, and the whole internet. This broader context makes possible doing things beyond the immediate home environment: tracking air quality issues, localized car emissions, and environmental pollution; customizing or personalizing uses of data from hospital equipment or medical records. This is such a huge idea that there are enormous numbers of events and spaces around the idea of coding for solving healthcare problems.

Google Search: (hackathon OR hackerspace OR hacking OR codathon OR codeathon) (healthcare OR health OR hospital OR quantified OR self)

Maybe you’ve already done some home-gown coding projects to help you in your own life, but you didn’t think of them as being about health as much as just life hacks. There is a lot of interest in those types of home-grown solutions (and finding partners to code ideas other folk have) for exactly those types of projects. Planning, sorting, self-organization, reminders are all skills critical to executive functioning (a psychology jargon term describing these skills). These types of tools and fixes are being used and sought heavily in communities with ADHD, autism-spectrum disorders, mild cognitive impairment, dementia, memory loss, and more. What was a simple life hack for you might turn out to be just what someone else has been looking for. If our brains all worked the same way, we could build one self-organization tool that would work for everyone. Because we are all different, we need many different types of tools, in the hope that one of them will work for that particular person who needs it. At events like this, people who need tools like this might discover people who can build them, or already have.

Or maybe you are someone who has been hacking together bits and pieces of things to track or monitor or solve things for your or a loved one, or is using services like YouTube or Twitter in interesting new ways, but you aren’t sure if we’d like to hear about it. Well, YES! We don’t have unlimited space so we can’t promise a space to everyone with an idea, but we will surely try our best and can’t try unless we hear about what ideas you have.


Sewing

#UMSIMakerfest !!!

You might be surprised to find out that most makerspaces have some sort of sewing equipment and space. And you might not realize that sewing has much to do with health, aside from clinic robes and doctor/nurse uniforms. Well, there is a huge market in adaptive apparel, also called adaptive clothing. That’s just for starters.

Most of the adaptive clothing is focused on practical concerns, and sometimes people want to be attractive, too. There is a lot of room in the space of designing attractive and/or professional clothing that is easy to get in and out of for people with various abilities. The growing awareness of this is evident through recent fashion shows employing models with disabilities, and several projects focused on disability fashion.

Design and disability: fashion for wheelchair users

Disability Fashion: Does this wheelchair make my hips look big? Spinning in style! That’s how we roll …

The Disability Fashion Project

Fashion Without Borders Initiative

Stylishly Impaired — Well-Equipped Crips: disability, pop culture, fashion, technology.

For some people the concern is that they need help from someone else to get dressed, which presents one set of challenges. For other people, they have reduced mobility or strength or an injury, and need alterations to existing garment styles to be able to manage getting dressed on their own. Imagine not being able to get dressed by yourself, and you’ll quickly realize the importance of adaptive clothing for personal independence. I encountered this challenge myself last Fall when I had a shoulder injury. I had such little range of motion with my dominant arm that I could only get dressed with one hand. That meant I needed all front closures for all garments, and all garments needed to be (very) loose-fitting, but not so loose that they wouldn’t stay up. I had some clothes that fit the bill, but not the right mix to make for a practical work week wardrobe.

Whether with a temporary injury or a permanent health condition, the challenges of designing attractive and functional clothes presents some deeply intriguing opportunities for really creative people with some sewing skills. One of the most fascinating examples to me was of a coat for persons in wheelchairs. I was unaware that often they also have problems using their hands. The solution was to sew the coat with ‘mittens’ sewn onto the end of the sleeves, ones that could be zipped up when needed, and when not needed, unzipped and folded back to look like a cuff. How creative!


Wearable Technology

The Mystery of IdentityCool Toys Pic of the Day - Maker Movement Meets HealthcarePic of the day - Wearable Tech at #FoolMoon
Ann Arbor Mini Maker Faire 2013Cool Toys Pic of the Day - Maker Movement Meets HealthcarePebble Pals

The phrase “wearable tech” is fairly new, a few years old, but the idea of it is ancient. Eyeglasses are wearable tech. Slings for broken limbs is wearable tech. So are crutches and canes, in a sense. Wristwatches are, definitely! Now, we have smartwatches to go with our smartphones, and phones are wearable technology! You can add in sensors, like these to track heart beats, relative position, or location. Many folk I know think of wearable tech with GPS (global positioning system) as being for geo-caching games, but it is used possibly almost as much for tracking children or persons with dementia who’ve gone wandering. The possibilities here to connect tech to health and well-being are virtually infinite.


Wood Working

GO-Tech Meeting at Maker Works

Yes, woodworking. Like most of these, this goes two directions. Maybe you’d like to talk about how you designed a lightweight sturdy portable DIY wheelchair curb ramp, or a portable wheelchair ramp for homes. Or an extra gorgeous in home ramp. Or a custom shelving solution for accessing hard-to-reach or heavy items for someone with mobility challenges. Or a wall-mounted flip-up flip-down lockable railing for someone living in a small space with occasional balance issues. Or how you designed an accessible building from the ground up — maybe a “treehouse” or playground for a special kid, or maybe an entire house. Maybe smaller projects. Woodworkers and people working in 3D printing could easily collaborate on sharing or modifying patterns for simple assistive tech. Those assistive tech spoons and grippers being made on 3D printers aren’t terribly sturdy, but if you made them out of wood, they would be both sturdy and beautiful.

On the other hand, maybe you’d like to talk about what modifications and accommodations were needed to make a wood working studio accessible and usable and safe for a person with multiple sclerosis or in a wheelchair. Or what type of modified grippers you used for lathes and die jigs.


MORE!

You can take these ideas a lot further than I have here. Arts and crafts are therapeutic for stress reduction, but also can be used to teach core science and mathematics skills, probably health information and skills, too. Origami concepts have been used widely in health sciences from making more powerful flexible batteries (which could someday be used in bio-implants) to designing anatomical models, to folding of molecular processes and nanostructures. You can even make a microscope with paper crafting, and gaming VR systems! Sustainable gardening and urban foraging connect to public health through addressing diet, nutrition, access to healthy local foods. There are so many ways in which we can use the DIY approach to improve health, for ourselves, for our loved ones, for our community.

GO-Tech Meeting at Maker Works