CAD-assisted Drug Design Using DNA Strands January 1, 2013Posted by stuffilikenet in 3D Printing, Applications, Awesome, Geek Stuff, Science.
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Scientists have developed a CAD drug development system that uses synthetic DNA as a programmable molecular substrate. These strands of synthetic DNA can be constructed to have any sequence of bases. And, because complementary sequences of DNA are mutually attractive, synthetic strands can be created with sequences that cause them to align with one another and bind to form nanostructures of virtually any shape. If the DNA strands are bound to other molecular species (say, tumor-killing molecules) before self-assembly is induced, the tumor killers can be pulled into desired locations by the DNA strands during self-assembly.
In other words, LEGO for molecules.*
This is paid for partly by NSF funding, but curiously enough a private company seems to have a lock on it. Parabon Nanolabs™ has simplified this concept down to CAD-based software for the budding mad scientist. The Parabon inSēquio™ Sequence Design Studio graphically enters designs and then determines the DNA sequences that will self-assemble into that design.
The graphic editor lays out a nanostructure visually. Users can rotate and bend strands, define bindings between base pairs, and copy and paste sequences and structures between design documents. The cloud-based number-crunching uses a bunch of known wet-chemistry values for the binding energies and calculates the complex molecular interactions required to make the molecule desired.
Neat, huh? This would be entirely impossible for a human to do, ever; it’s billions of calculations that need to be made and complex rules to be followed.**
Still, how they will mock up the synthesized molecules themselves should be an interesting technical feat; I would really like to see the execution of this, rather than a neat CAD program for molecules.***
* Some assembly required.
** Another reason not to be a chemist.
*** It’s not impossible; use synthesizers to make the short pieces, PCR copy them, keep them salty enough that they can’t self-assemble before all the other pieces are made, mix together and pray. The devil is in these details. Maybe we can get Rob Park to do it.
Android Development Environment—Part Two December 15, 2012Posted by stuffilikenet in Applications, Geek Stuff, Uncategorizable.
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In which Our Hero has a revelation about printed matter.
I bought a copy of Sam’s Teach Yourself Android Application Development in 24 Hours (2nd Edition) a while back because it was up to date (more or less) and I felt it would have the requisite instructions for correctly setting up the Android development environment for me, the rookie.
I stand corrected. the development cycle for android is pretty swift, and the book was obsolete before I touched it…also makes too many assumptions about the clarity of its instructions—but I digress.
The correct way to set up your Android development environment (and don’t listen to anyone who tells you otherwise) is to download the ADT Bundle from android.com (follow the link) and install that. Period. Seriously: if you try (and I did) to set up each piece individually you will find yourself a broken, bitter wo/man. It just doesn’t work to do it that way. The Bundle contains pretty much everything you need. I installed it to my (present from stepdaughter) Batman-shaped USB thumbdrive, and it seems to be working properly.
Finally. I had a lost weekend over this, and one weeknight. Harken to my tale of woe, and let your Bundle flow.
Spanish Flashcard Android App Review September 29, 2012Posted by stuffilikenet in Applications, Brilliant words.
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I plan to review as many Spanish language flashcard programs as are offered for FREE on GooglePlay. If they all suck, I will make a pay version myself and sell it for US$0.99. Yeah, sure. What are the odds I can do better with nearly no knowledge of Spanish and with severely limited Java/Android skills (I already made one, but I would have to re-write it for JAVA)?
4001 Spanish Verbs by email@example.com is not really a flashcard program; it is a FREE conjugated listing of 4001 verbs (like it says), right down to the pluperfect subjunctive. Gods, I can barely remember what that means, let alone find the time to require myself to memorize it (again). Very nice, but a little ahead of my needs. Seems very functional enough, though. I will use it later, when I actually have mastered a bit more Spanish (quite a bit).
Spanish Vocabulary by Robert Muth is a very nice package with rather more sophistication than I expect from a FREE program. It is divided into topics, remembers your ability to remember each word/phrase, alternates between Spanish first and English first and provides example sentences for context. Very slick. Seems pretty functional to me. I presume there is a pay version, but it’s unobtrusive, so far. The advertising that supports this FREE version is unobtrusive, appearing only on the selection page (Adjectives, Everything, Top 100 and Verbs. The pay version probably has more categories, if there is a pay version). This one is pretty nice. I’ll use it as well.
LangLearner Spanish by langlearner.com starts by downloading (over the air!) 250MB of Spanish lessons, over and above the installed application. Turns out to be pictures and audio to illustrate the phrase. Pretty, but the photos don’t add anything to the experience, although the pronunciation by a native speaker is certainly useful. There are thirty-two categories and they are pretty well illustrated, but only the first six are in the FREE category; I am not reviewing the paid application (until it’s provided to me FREE).
All in all, not bad; the pictures might help, too, now that I think about it. Who knows how the memory of any one person works to recall particular phrases?
Spanish Flashcards Free by RFX Labs is also a preview app, offering a paid version with 1000 words (sound familiar?) in 22 categories. And it displays ads even in the FREE version with not many words…skip this one, I think.
Spanish Flashcards by Bradley G Hohn is a much better bet, with 3500 words and phrases, text to speech support etc. however, the reviews on the GooglePlay site are kind of unkind, mostly about the translations. I can imagine that people’s interpretations may differ, but without being able to evaluate the reviewers’ skills in Spanish, I can’t tell much more—remember, I’m a complete novice.
Spanish Flashcards by movinapp.com was free, and the first forty cards looked [gods, it's hard to type one-handed while petting demanding cats] right and I knew their translations were more or less correct. Very nice. The translator’s computer voice was pretty good, too, using the Android engine (which it downloaded as soon as I hit the first "play the phrase" key). I will continue with this one for a few days and see where I get with it, treating it like I would any other app I was debugging. Wish me luck.
In my first session I noticed that the synthesized voice, which had received some negative reviews was actually pretty pleasant. It may be that I have a very nice new Android 4.1 system to operate it on, however. I am told that the speed of the synthesizer can be adjusted, but I haven’t had the need. The translations were also knocked in the reviews, but I can’t see anything that isn’t more or less correct, so I give that a pass as well. The cards are grouped in categories: Basic Expressions,Greetings, Courtesy, Phone, Time, Dates, Chat, Shopping, Airport, Help, Directions, The Weather, Health, Number and Internet; as many as seventy or as few as a dozen. One thing I notice when perusing the categories is that the application offers to download the speech synthesis module for Spanish each time I switch a category. You can back out of the screen easily enough, but you shouldn’t have to do that, since the application apparently knows (or the download screen knows) that you have done that already. Not terribly polished I admit, but if that’s the only bug I find I will consider this FREE application a very nice package, indeed.
All in all, I think this flashcard package is pretty sweet. The largest drawback might be the small advertising area in the lower right area of the screen, which is always updating itself. This could be a drain on someone with a limited data plan. This is, of course, how this program can be FREE–the authors are selling your eyes to the Internet, just like any commercial webpage does. I like this app and will use it for a while.
HTC 8125 Hacking July 2, 2012Posted by stuffilikenet in Applications, Geek Stuff, Uncategorizable.
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in which Our Hero attempts to use SDHC cards with his Cingular 8125, Windows Mobile 5 phone, a.k.a. WIZ100 or HTC Wizard. A harrowing tale of suspense, long hours in front of a monitor reading the forum at xda-developers.com, eyestrain and terror at the thought that I may have to flash the ROM altogether.
So, first I tried to simply hack the system with a bunch of different SDHC hacks, which in fact killed my SD card reading ability entirely.
Well, I don’t really love this phone anyway, except that I had it hacked up pretty much the way I wanted it except for the 2Gb limit to my SD storage (see previous AD2P post, below and KanaFlash and Spanish FlashCard App). So, I figured I might as well look at replacing the ROM with something a little more modern with SDHC support baked in…like Windows Mobile 6.5. Good idea, right?
This is an enterprise fraught with undreamed-of perils. First, CID-unlocking (the phone from ATT, so I can load whoever’s ROM I want) and all this involves. I need to do this if I have G4, but not if I have G3. I could have sworn I had G3 yesterday when I was fooling around with the SDHC stuff, but today I seem to have G4. Ugh. I can tell I do because my IPL and SPL (bootloader stuff) is 2.25.0001—the three zeros mean G4.
I could have sworn there were two zeros there yesterday, and I wrote it down in my notebook which I left at work…grrr [I checked; it WAS two zeros then]. Anyway, these details are hugely important, since I could brick this puppy (and have a great excuse to get a nice, new phone) by using the wrong loader, image or both. I live in fear, since there is no extant FAQ on just how to do this, and these details count. However, there is a forty-five page forum thread on this topic at xda-developers.com.
I should finish reading it about August, I think.
So, here’s what I know:
Device Model Cingular 8125, CID WIZCNG01, DOC G3 / G4, ROM Date 2006 11 May, IPL/SPL 2.25.0001, ROM Version 22.214.171.124, Radio Version 02.25.11, OS 5.1.195, Build 149126.96.36.199, Protocol version 188.8.131.52, ExtROM version 184.108.40.206
If it’s a G4 phone, then I need to unlock it from CID using the IMEI number under the SIM card, and a for-pay utility here. Then I could load the ROM I got here [turns out I can use a different IMEI that I also found at xda-developers.com], assuming it is a G4 which uses a different ROM loader than the G3–no small difference, that. Once again, masonry is a real possibility.
You would think that a clear-cut version of what is now very old technology would be apparent; no my brothers, not one malenky bit. Ancient technology such as this (ca 2007) is best not messed with.
Exciting update: I hard reset it, and got my (old) functionality back…a mixed blessing. In the meantime, I found that I can pre-pay ATT $25 a month for 300 minutes, unlimited texting and unlimited slow data, so that’s one thing I’m going to do Real Soon Now. And pay full price for a nice Android phone, for which I can also write my little programs, albeit in java.
Had to get this all off my chest, as it ate a great deal of my (limited) attention for a while.
I Should Explain This to Normal People April 10, 2012Posted by stuffilikenet in Applications, Brilliant words, Geek Stuff, Publishing Tools, Video.
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I test (other people’s) code for a living, which often involves boring, repetitive keystrokes, mouseclicks and other user actions before producing a desired result (i.e., showing me where it’s broken). This can be automated in Visual Studio 2010 easily, but checking that the desired result has been achieved can be somewhat more difficult or at least non-intuitive. The process of checking a result or condition is nicely described in this video.
Win CE Audible Spanish Flashcards January 20, 2012Posted by stuffilikenet in Applications, Awesome, Brilliant words, Geek Stuff, Publishing Tools, Toys.
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This is an update of previous work on the Win CE Spanish Flashcards program I wrote earlier. I find that driving while using this I would look away too often from the road, which is stupidly unsafe. The new and improved program here will speak the word displayed in a sexy Spanish lady’s voice while displaying the word. You can turn it off by pressing the Options button on the bottom left of the screen. Everything else works as before.
I ran into a nasty little problem while creating the .CAB file which contains the installation, since I have a thousand sound files, which is more than the cabwiz.exe which comes with Visual Studio 2008 can accommodate…and the error code for this defect is completely unhelpful, in the grand Microsoft tradition:
Error: File c:\users\[me]\appdata\local\temp\wizbbe1.inf contains DirIDs, which are not supported
ERROR: The Windows CE CAB Wizard encountered an error. See the output window for more information.
It turns out that VS2008’s cabwiz.exe chokes on more than 998 included files, and this application has 1057. The workaround is to download the SDK for Windows Mobile 6 and use the cabwiz.exe (and the cabwiz.ddf) from that version instead (C:\Program Files\Microsoft Visual Studio 9.0\SmartDevices\SDK\SDKTools\CabWiz.exe and CabWiz.ddf with the ones under C:\Program Files\Windows Mobile 6 SDK\Tools\CabWiz). No problem once I had done this.
Here is the all-new singing and dancing Win CE Spanish Flashcards App.
KanaFlash, a WinCE Kana Flashcard Application December 15, 2011Posted by stuffilikenet in Applications, Awesome, Brilliant words, Geek Stuff, Japan, Toys.
KanaFlash displays hiragana and katakana characters and shows their English equivalents, and even pronounces them for you unless you toggle the sound off with the English/syllable name button. An updated version will have pronunciations of yet more syllables…really it will. I promise. Honest.
Win CE 5.0 Dictation Application December 15, 2011Posted by stuffilikenet in Applications, Awesome, Brilliant words, Geek Stuff, Publishing Tools, Toys.
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I never found an application which would automatically take a note for me when I would just talk to it (without having to push a button first), so I wrote one. Be happy for me; this is my second useful application for WinCE and I’m actually quite thrilled. I have a long commute and often think of little notes I should jot down, and have no hands-free way of doing this…until now.
Dictation gives me sixty seconds of WAV-file goodness, with the recording beginning as soon as it opens. I used the “Voice Speed Dial” in the Settings menu to record my voice saying “Dictation”. This device opens the application for me, and the app does the rest, leaving the WAV file with a timestamp-based filename in the Dictation directory when the Save button is hit (take your time; it won’t go more than sixty seconds). I can then restart the recording and get another WAV file with the second button for the next result and so on, but this requires button pressing. A third button closes the app, which is oddly enough required for this application so Voice Speed Dial can automatically reopen the application later1, when inspiration and/or regret strikes.
1 WinCE applications do not usually close by themselves, which can eat up a lot of memory if you don’t manage that yourself. Of course, this comes in handy if you want the FlashCards application to keep your place, as I do.
Adventures in C# .NET Programming November 4, 2011Posted by stuffilikenet in Applications, Awesome, Brilliant words, Geek Stuff, Publishing Tools, Toys.
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I promised a while ago to write a review of James Foxall’s Teach Yourself Visual C# 2008 in 24 Hours and I meant it at the time. Instead I have found that I learned enough from his first book Teach Yourself Visual Basic 2008 in 24 Hours: Complete Starter Kit. The two languages are much alike and the .NET framework supports them both. I am probably going to stick with C# since my company uses it in its various scientific applications. The other reason is that I need to learn a heck of a lot more than how to use the interface, so I started to program a flashcard program for Spanish.
Like all frail, elderly types I have real trouble learning a new language so I looked for a flashcard program with mixed success. Professional programs for my (also frail, elderly) phone (a WinCE 5.0 job) cost a pile and had really tiny fonts. I decided to make my own.
I don’t know that I need to tell you how hard this was or how many times I had to ask for help from wiser minds (thanks Ben, Shabnam and Mark!) with the requisite 10000 hours under their belts. But I muddled through somehow and even figured out what went wrong on the last few things without help from my cow-orkers (hyphenation intentional).
Here’s how it looks on the emulator:
You can see that it’s set for the second set of flashcards (twenty words a set, fifty sets). The top button flips to a new Spanish word. The bottom will show you the English equivalent if you press it. My phone and the emulator have trouble with accented Spanish characters, but that’s a job for the future.
I learned to parse files from WordsGalore, a free flashcard program for PC which I strongly recommend, with support for Spanish, Chinese and Korean. I haven’t included much of WordsGalore’s marvelous functionality such as the elimination of words in which the student is already confident, but the phone probably can’t handle it (not just that I can’t program it, yet). I learned the basics of debugging using Visual Studio 2008. I learned to plagiarize by examining other’s code (“only please to call it ‘research’”). I learned how to make .CAB files for easy distribution (look here). I learned that my cow-orkers are very patient with me, for which I am truly grateful.
Exciting update: I modified it to include a switch button which allows the English words to display first instead: