Today’s Apple Feedback: Back-to-My-Mac is unstable

I use Back-to-My-Mac a lot to connect to my laptop @ home or my iMac @ work. I’ve lived & worked in 3 different places, owned multiple home & work computers, & had multiple internet providers. I’ve been using Back to My Mac since it was a feature of Mobile Me. Before that, I was using Chicken of the VNC since the early 2000s. And while it was free, I’d been using LogMeIn as a backup when Back to My Mac wasn’t working – and that was a *lot*. LogMeIn always worked when Back to My Mac didn’t. Could you please make it more reliable? I’m tired of seeing this message:

This week, I’ve tried to log into my home laptop 4-6 times. It usually fails the 1st time & works when I try again an hour later. Not today though.

Update:

Well, frustrated with no working “Back to My Mac” (hence, BTMM) for the past week or two, I wanted to convince Apple that this is a real problem, so I temporarily set up external screen sharing and sent them an update with screen-caps as proof that BTMM should work, but doesn’t.  I blotted out the sensitive bits and of course…

I rarely get Back-to-My-Mac (BTMM) to work. Here’s proof via screen caps that BTMM should work, but fails:

 

Initiate via BTMM:

 

Waiting via BTMM:

 

BTMM error:

 

Initiate via URL:

 

Credentials via URL:

 

Success via URL:

 

Remote BTMM prefs:

Hopefully Apple will make BTMM more reliable at some point…

Today’s Apple Feedback: Siri can’t find my contacts

This same issue happened last week when I told Siri to call my mom, but when that happened, I was driving and didn’t bother to screen cap. This time it happened when I tried to use Siri to text my wife while walking. Siri responds saying she doesn’t have a phone number for her. See my screen caps below:

Siri saying she doesn’t know my wife’s number:

The contact card for my wife with her phone number (which I blacked out for privacy):

I just tried using Siri again to text my wife and this time, it worked, so I’m not sure whether this is a 1-time thing for each of my contacts or whether it’s going to happen to me randomly now.

Of course, you might say there’s a typo in the name or something, but I told Siri to text “my wife” each time – one time that worked, and the first time, when it didn’t work.  Each time, it correctly identified my wife’s name.  The only difference is that the first time, Siri claimed she didn’t have a phone number for her.  I checked my contacts, and there’s no duplicates and there’s not anyone’s name that’s even remotely close to my wife’s name.  Same goes for my mom.

I’ve noticed some weird contact card issues lately and I’m guessing it’s related.  I had some duplicates pop up.  I had edited a bunch of cards about a week ago and over the past week, I’d noted that some of the info I’d manually entered was missing – like my wife’s new phone number.  Yes, she got a new number, and you might say that could be related, but none of my mom’s info had changed and Siri forgot her number a few days ago.

Today’s Apple Feedback: Space-Switching Inconsistency

I use a lot of desktops (formerly know to OSX as “spaces”).  Each desktop has windows open relating to a different project and when I split my time between two different active projects, I switch desktops.  This occurs infrequently, but maybe a couple times a day.  I find it rather disorienting and disruptive when I accidentally get thrown to an apparently random desktop for one reason or another, so I have set my system preferences accordingly, and that works fairly well for every application… except for the Finder – the app I arguably use most frequently. If you use the dock to switch apps instead of command-tab, and you frequently use multiple desktops, you may have noticed this inconsistency that frsutrates me every day, and it’s exacerbated by the fact that the animation doesn’t intuitively tell you how far you have to go to get back to the desktop you were just on.  Thus, today’s Apple feedback:

Finder’s Space-Switching Behavior is Inconsistent with Other Apps

In the Mission Control system prefs pane, I have “When switching to an application, switch to a space with open windows for the application” *UN*checked. I like that if I click any app in the dock twice, it will still switch spaces despite that setting, yet clicking it once will not switch spaces (as long as it’s not the foremost app). However, this behavior is different for the Finder depending on whether or not there are any finder windows open on the current space. If no windows are present and the finder is not foremost, a single click of the app in the dock will switch spaces despite the system preference setting. This is inconsistent because the same conditions for any other app (e.g. Safari) will not do this any stay on the current space. This inconsistency disrupts my productivity.

Filtering Metagenomic Errors

People know that DNA sequencing technology has advanced and I think that the common lay-person’s perception is that we can sequence a whole genome, each chromosome, from end to end.  In many cases, that’s possible, but it’s still a monumental effort.  Notions of a “$1000 genome” belie the difficulties in full genome sequencing.  When you hear in the news that we can sequence your genome – services like “23 and Me”, you think that we’re getting the whole picture, but we aren’t.  We can sequence multitudes of short sequences very quickly and what we get is then mapped to a reference genome (which was one of those pain-staking efforts).  But a (what I would consider) large portion of what is sequenced cannot be mapped and those that are mapped can have many inconsistencies – because one person’s genome may have a certain number of shuffled portions and subtle differences.  AND you could even have two different cells from your own body possess 2 different distinct genomes.

Then there’s metagenomics – where we sequence multiple organisms all in one shot.  You take a sample of water, dirt, or a swab from the flora of your mouth and you extract the DNA from all the microbes there and sequence it without a reference to map any of the resulting sequences to.  In this torrent of information, we lack certain controls typically used to gauge quality of the sequence.  As with all machinery, there is a margin of error.  Sometimes a sequence that comes out has a typo, an A instead of a T or an extra G, or a missing C.  When we’re sequencing one organism, we can compare a piece of DNA with other copies of DNA with the same “word” and the error gets out-voted and ignored. It’s like having 100 secretaries type up the same document in a foreign language that you don’t know.  If 99 secretaries type the first word as “Que” and 1 of them types “Uqe” or “Quee”, we can pretty safely say that the correct word is “Que”.  But if each secretary is randomly given 1 of 25 different documents to type up – each of which is purposefully slightly different, it’s not so easy to dismiss “Uqe” or “Quee”.

But if we know that the “e” key is slightly sticky and prone to typing double letters every once in awhile, it becomes easier to dismiss an instance of “Quee”, and that’s what this post is about.  But what if there actually is a word such as “Quee” and we’d be dismissing a real word because we assume all rare occurrences of a double ‘e’ as a mistake?  We can figure this out by using a control to measure how frequently this type of mistake occurs.  As long as the occurrences of “Quee” fall into that general frequency or below, we can reasonably assume that it’s a typo.  If we see “Quee” twice or three times as many times as we would expect if it were a typo, we might conclude that it’s a real word.  And that is the basis for my recent paper and related software.

Typically, these sorts of errors are filtered out by first grouping all the most similar “words” together and then selecting the most frequent one as the representative of that group – assuming all others are errors of it.  However our method forgoes the clustering step and first tries to measure the frequencies of each type of error present in the data – the ones we are fairly confident are errors.  Then we look at the most similar words and determine whether one word could be an error of another by measuring how frequently each word is encountered and determine how likely the less frequent word is to be an error of the other by seeing whether it falls into the typical error rate/frequency we measured earlier.  We call our method “Cluster Free Filtering”, or CFF for short.

There’s a lot more to it, but that’s the basic concept.  You can get the nitty gritty details from the paper or even try out CFF for yourself if you have some DNA on your computer.  It’s freely available.  Note though that this is software specific to 1 narrow realm of metagenomic analysis: analysis of 16S rRNA variable regions where all the short sequences are very similar at the starting point.

Reminder Hack

Have you taken advantage of geo-fence triggered reminders using Siri?  You can say things like “Remind me to take out the trash when I get home” or “Remind me to stop by the farm stand when I leave” and Siri will set a geo-fence triggered reminder. I use this all the time and I love it, but it’s a bit too late to remind you to bring your work out clothes when you leave, as the reminder tends to happen when you’re already in your car a ways away from home.  The reminders for when you arrive are more useful, but they can go off when you’re busy driving as well – with plenty of things to distract you before you get out of the car.

There are probably lots of ways you can hack your own more accurate reminders, but I am setting off on an experiment to test out one: WeMo motion-sensing notifications.  WeMo makes these motion sensors designed to turn on and off lights and what-not, but you can also set it to simply send yourself a message.

WeMo Motion Sensor

I’m setting out to play around with it to see if I can get it to give me accurately timed reminders right when I need them.  You can create rules that govern when a notification is sent, such as days/times when a notification can be triggered by motion.  You can also set it to do things when you’re “away” or “home”.  You can also hook it up to IFTTT, which allows you to set all sorts of different triggers and actions.  I might try to get it to turn on my window A/C unit when I leave work for example.

There are drawbacks to doing reminders using motion sensing: the cat or my wife could set it off.  It doesn’t know exactly when I’m leaving.  I could just be going out to put out the trash.  I can mitigate this by having it only remind me about bringing something I need to work by only going off upon sensing motion in the morning when I’m at home.  I also can’t use Siri to set these reminders (unless I were to jailbreak it or set up my own Siri server).  But I imagine that the ability to create custom Siri commands might be in our future…

I will post again once I have some results of my little foray into making more accurate reminders.  If you use your own trick for creating more timely reminders, please comment below.

Picking up where blog.com left off

This blog is a continuation of my blog.com version of this blog.  That site was continually going down, to the point where every time I tried to create a post, I could not access the site or my posts had gone missing.  Perhaps at some point I will try to transfer those entries here.

I mostly post stuff about swing dancing and computational biology.  As I write this however, hype is building for the new Star Wars movies, so I might sneak in a post or two here about my beloved films.