Binder Clips have been the subject of many many DIY inventions. Even weapons of not so massive destruction. They’ve been a medium for sculpture. Why not then use our bendy metal friends as building blocks for puzzles? As a kid I loved those metal ring tanglement puzzles and I still have my Rubik’s Snake!

My first puzzle is an 8-clip puzzle made by linking clips clip-to-clip to form a ring. Once you have the ring formed, you should be able to achieve at least 5 distinct shapes, and possibly more. My theory is that because each fold involves half the clips, the practical limit on the number of folded shapes is something like log2(N) which would be 3 for our 8-clip puzzle. Further shapes are achieved by manipulating the free clip arms.  If you build your own variation on this puzzle or find additional possible bend shapes, be sure to let me know.

Update: My second puzzle is a kind of helix shape that transforms into a symmetrical square box shape. Unlike the previous puzzle, this one forms a flat-laying double layered box and requires a fair amount of thinking in terms of when to fold the clip arms. It’s surprisingly tricky, though this puzzle appears to have only two possible final shapes (when folded flat).  Maybe someone will be inspired to build and play with these puzzles with their (appropriately aged) children, or by themselves at work on a slow day. Here’s the new puzzle in action:

Here’s a quick video of the first puzzle in action. The box shape as shown in the video can be formed without the “handles” sticking up by folding the arms in first. The background music is a snippet of an old track of mine that seemed to fit nicely. Sorry for the noise/jumpiness in the video — I was using this as an excuse to learn how to edit and shoot a video using an android phone and Ubuntu linux. I used kdenlive for the editing, but I ended up with black bars on either side of the video due to shooting portrait and having to rotate. Next time I’ll know to shoot landscape. The camera was held up by a binder clip during shooting. :)

Bad news: you don’t own your own DNA because the human genome is nearly entirely patented. These patents present a legal barrier to life-saving biomedical research and diagnosis. The good news is that on April 15th the US Supreme Court will hear arguments in a landmark case focusing on human breast cancer genes. Please take this opportunity to speak up and let the justices know that the public cares about “genomic liberty”.

Visit the website of the US Supreme Court Public Information Office and send a message. Here’s mine:

Dear esteemed justices,

Like many curious children, I grew up wanting to make the world a better place by making a contribution to biomedical science. After years of study in pursuit of this goal, now I am told that my good intentions may amount to an illegal transgression! Please end human gene patents so that the millions of people like me who want to improve human quality of life can do so without fear of patent infringement liability. Such fear can only serve to stunt the advancement of human health sciences.

Humans are born with their DNA, and so it seems right that we should own the information within our own bodies and reserve the right to use it to improve our health, or the health of others.

Thank you for your attention and your service to our country,

Daniel Packer

Student at Hunter College

Get the word out by sharing this post and sending these links to your friends and colleagues.

Excellent coverage of the issue by 60 minutes (thanks Ron)

Supreme Court Public Information Office contact page

Information on the ongoing landmark case and the April 15 hearing

Research paper on humane gene patent coverage (free pdf) and Press Release with a good summary

By the way, I didn’t coin the term “genomic liberty” but I think it’s apt!

In the video, the instructor puts a problem up, steps aside, and then invites the student to solve it. On the Note 10.1, I can pause the video, draw out the problem, solve it in S-Note, and then resume the video. The effect is like a classroom tailored to my learning style. I can change the relative size of the two windows with the slider in the middle. If I need to maximize (for example to switch to another video), I can do that quickly, and then pop the window back into place. Many top apps now support this multi-window feature, though not all do. I found portrait mode was the most comfortable in which to do this, but for textbook in a split window I prefer landscape.

What I’d like to add to my virtual classroom experience is a real time dialog with instructors and students — something that is often missing even from classroom settings (especially in large classes). I’d also like to have a large searchable e-book and academic paper database at my fingertips so that any conceivable relevant reference could be pulled in real time. These things can be sort-of accomplished with online forums and various web sites and apps, but integration will follow as operating systems focus on metadata and multitasking/interoperability.

Online educational materials are getting to the point where they’re good enough that they can be used as gold standards. Professors will regularly reference Khan Academy videos or Wikipedia articles and schools like MIT and Stanford are really pushing free online education. To sample the kinds of high quality educational material being offered online, check out this neat list managed by the Director & Associate Dean for Stanfords Continuing Ed program.

As online media gets more interactive (a stated goal of some educational sites), the classroom will only get more portable. I hope that more schools start to adapt to this new mode of learning because I think it will appeal to a broader range of students than the traditional classroom experience, and will probably make professors jobs a little easier. It’ll certainly make backpacks a lot lighter.

Here’s to the future that is now. :)

]]> http://danielpacker.org/galaxy-note-magic-split-screen-video-and-notes/feed/ 1 http://danielpacker.org/short-meditation-on-going-paperless-surface-pro-vs-galaxy-note-10-1/?utm_source=rss&utm_medium=rss&utm_campaign=short-meditation-on-going-paperless-surface-pro-vs-galaxy-note-10-1 http://danielpacker.org/short-meditation-on-going-paperless-surface-pro-vs-galaxy-note-10-1/#comments Mon, 04 Mar 2013 04:12:05 +0000 Daniel http://danielpacker.org/?p=1448 Wherein I attempt to live my longstanding dream of a paperless world where all information is at my fingertips and my desk is free of massive piles of dead trees. Call it Ender Wiggin syndrome if you like (yadda yadda first world problems yadda yadda). As a student, I regularly work with handouts, assignments, exams and quizzes, and textbooks/workbooks. Being a student isn’t that different than being an office worker (from what I recall…), so I figure this might resonate with a lot of people.

The Three Missing Pieces

Scanning. In order to go paperless I had to have an efficient way to get lots of paper into PDF files so I could read/edit them later.

Storing. Considering I access documents on multiple computers and connections, I needed a safe and efficient way to store, distribute and access files via the infamous cloud.

Annotating and Note Taking. My workflow involves marking up PDFs for notes or assignments, as well as typing and drawing notes and work during and outside of classes.

Digitizing The World

In order to get paper documents into files I used Handy Scanner and CamScanner software on my droid phone. You basically flip the page, take a photo, flip the page, take a photo, etc. Finally, you fix up the pages in a preview mode and save (or share) the PDF file. This works most of the time, but I did have issues. For example, after scanning a 170 page lab manual, I switched to another app, and lost my entire scan. Why the software wouldn’t save state I’m not sure, but it didn’t. If you’re careful though, this is a better scanning solution than a flatbed scanner.

If you prefer not to do your own scanning, there are services that will digitize books fairly cheaply for you. I prefer to do my own dirty work because I like the instant gratification. I was able to scan at least 10 pages per minute.

For single-page scans, a simple photo with the built-in camera app on your phone would be plenty. If you’re doing multi-page PDF scans, you’ll want some sort of app, whether you have an iOS device or an around device.

Edit: A Facebook friend suggests this scanner, which can feed multiple sheets. Sheet-fed scanners are definitely an option if you can remove the binding of whatever you’re scanning and afford the price tag.

Storing Stuff

Paper doesn’t disappear when you turn around, but computer files sort of do. You’ll want a safe and efficient way to store and retrieve all your paperless stuff. My poison of choice is Dropbox, which is a painless and (so far) free solution for cloud storage. Dropbox can sync files between your computers and even your droid (with Dropsync) so that you have one local copy and one cloud copy at all times. It’s best to back up all your stuff to a backup drive no matter what, but a cloud account gives you one extra layer of protection and a lot of functionality.

Dropbox (this is my “affiliate link” so please use it if you sign up) gives you 2GB for free as far as I recall. It so happens that Dropbox gifted me a 2-year 50GB allowance on top of the free storage I already had for being a “Dropbox Guru”, which I guess means I got a lot of free stuff for using free stuff a lot… No complaints.

When you scan documents or retrieve documents for annotation, you’ll want the middle-guy to be your Dropbox/cloud account. Most apps now support sharing to and from Dropbox and other popular services, so that’s a no-brainer.

The Paper Replacements

Galaxy Note 10.1: At $500, the white 16GB Note 10.1 didn’t break my budget. It’s relatively light compared to the Surface Pro and easy to whip out on the train, or in class. PDF reading is good in landscape mode, but you can’t fit a whole letter size page on the screen and read the text comfortably (the page becomes 1/3 the size of the screen). For half pages at a time it’s great. In portrait mode you can fill most of the screen with a whole letter size page, but the text isn’t pretty. It’ll do the job, but it’s not going to be fun for hours and hours of reading. For annotating and reading PDFs I used RepliGo reader which is a great piece of software. It basically marks up PDFs and reads them very well and retrieves/stores to Dropbox very easily. For note-taking I used S-notes which is alright, but the lack of auto-save has caused me to lose several full class notes and I’m reticent to keep using it, though it works fine otherwise. I’ve found the S-note app to be very handy for capturing spontaneous ideas.

The killer feature for the Note 10.1 is that  in landscape mode I can read a textbook in one half of the screen and write out problems on the other half. This is fantastic for doing math, chemistry, or other calculation-heavy work, or even for taking notes on something you’re reading.

In short, the Note 10.1 keeps things simple. When it comes to replacing paper, it’s a matter of being as simple as possible. Paper works because it’s simple, and any solid paper replacement must offer the same.

Surface Pro: At about $1170 for the machine and keyboard, my wallet is hurting a bit. Compared to the cost of a tablet and a laptop, it’s not bad, and the hardware itself is beautiful. The 1920×1080 full 1080p HD screen is gorgeous. Unfortunately, text is too small, or blurry, even for my perfect vision. App interfaces and text quality is inconsistent and finding important functions and settings are trial and error. As a laptop, I found myself going back to my thinkpad for most situations like coding and writing long documents. The lack of adjustable screen angle on the Surface Pro (it has a one-position stand) made it rather awkward for desktop use and I found myself slouching. Watching netflix in bed however was a dream, and much more dramatic than on the Note 10.1. Until it toppled over and clunked me on the nose. Twice. Ouch. This thing is heavier than the Note 10.1 and less natural to use in general. The battery life is less than half that of the Note 10.1 in my experiences so far.

Off topic, but I was experimenting with running virtual Linux machines on the Surface and wasn’t able to get a 64 bit Ubuntu install going on Hyper-V. It was slow-as-dirt on Virtualbox and so was Debian. Maybe the 1GB I allocated wasn’t enough. Seemed like a bad sign, although everything else ran fairly snappily.

The full HD screen fits TWO-count-em-TWO full letter PDF pages in landscape mode and over one full page in portrait mode with extremely readable text. For PDF handling, the Surface Pro wins hands down. That said, the complications (read: bugs) of running a full blown desktop OS bog down the experience a bit, and android tablets are catching up with their own full HD screens. MS Office and OneNote are superior in functionality to the S-note application and the digitizer/stylus on the Surface Pro is lightyears ahead of the one on the Note 10.1. It’s truly delightful to make art on this device. I haven’t sketched in years, but was able to make this using the free Sketchbook Express app from the windows Store. I can only imagine what’s possible in the hands of a skilled illustrator!

Speaking of the Windows Store, there’s no way to be diplomatic. It sucks. The selection is extremely limited and it’s a mix of expensive mainstream apps and random things that seem to be mostly analogs of mobile apps from iOS and android but aren’t as useful. Of the apps I tried (Skype, Dropbox, Facebook, Netflix, etc.) only the Netflix one was as good or better than the Android counterpart. The Google Play store has a leg up here, though neither are as polished as the Apple ecosystem.

In short, the Surface Pro, as has been said in reviews, is not a great tablet, nor a great laptop, but it’s a beautiful and weird piece of hardware that should appeal to people who want the ultimate video player, or a portable art platform.

Conclusion

Things have sure come a long way from when I last tried this. Getting books and forms into PDF format is super easy. Marking up the PDFs is super easy. Storing and retrieving them safely and efficiently is super easy. Plus, it’s all cheap. Both of the devices I tried support reading a document while editing in another window, inputting arbitrarily complex math equations with the stylus, storing and retrieving PDFs from the cloud, and note taking and PDF annotation.

So, yeah, it’s absolutely possible to do away with paper. Android tablets like the Note 10.1 are adequate for the task, but the hardware and software is still a little rough around the edges. Higher resolution screens, more accurate digitizers, and more refined applications will all undoubtedly come down the pipeline as time goes on. High-end windows tablets are very promising, but need to build on the feature set of laptops before they can fulfill their one-device promise. Hybrids like the Lenovo helix seem promising and might be more appropriate for someone like me, though I still like having a lighter device to use for reading/notes. The iOS devices are super fun, but without any devices that support active stylus/digitizers, they are out of the running for now. I suspect Apple will eventually enter the fray and sell a pen-enabled device, but who knows.

The Surface Pro is definitely going back, much as I love it for doodling and movies. The Note 10.1 might stay. I’d hate to go back to waiting for another device, but I might just do that and see what comes out in the next few months. That’s all she wrote. Happy to field questions.

Above: The Broad Institute proudly displays a micro pipetter used by his holiness.

There’s been a lot of Stuff. This winter I attended a really fun workshop at MIT where dove into amazing topics like use of next-gen sequencing in transcriptome (RNA-seq) and epigenetics (CHIP-seq) research. It was an ambitious and intense week where we tried to touch on as many major fields in bio research as possible. The MIT game lab was across the hall from our computer lab during the workshop so we were able to stop by for a demo of their funky game based on relativity. Allegedly I was a staff at the three-week 2013 CMACS workshop on modeling atrial fibrillation, but I was really a participant in disguise. I’ve been absolutely obsessed with  chaos in biology and chemical diffusion as the engine of life since the workshop. CMACS has been amazing for me, between what I got to do last year, and all the people I met and ideas I was exposed to this year!

While at the MIT winter thing I met up with Dr. Tom Knight of Ginkgo Bioworks and he kindly to gave me a great lab tour (slideshow below). The level of automation in his lab rivals the Broad institute, minus the sequencers. Robots and barcodes everywhere. I’ll be going back to MIT this summer to work in Dr. Amy Keating’s protein lab. They’ve been working on some cool synthetic biology applications of their coiled protein library. It should be possible to engineer pretty sensitive transcriptional circuitry with those proteins. Dr. Keating and her colleagues seem quite motivated and curious and I really really look forward to joining up with them. I’m definitely going to try to get over to the Voigt lab and see what’s going on in bacterial computing (which is apparently one of my hobbies). Of course, I am anxious to return to Cambridge so I can finish trying every damned item on the menu at Veggie Galaxy.

Research-wise, I’m working with my mentor, Dr. Qiu and with Dr. Nishura at Brooklyn College getting a bit into RNAseq differential gene expression analysis in mosquito larvae. Catalyst is having us get together in groups and present some research this semester. Since earth scientists outnumber the biologists, we’re focusing on fracking which happens to be a pretty hot topic, especially in New York state.

Aedes Aegypti larva striking a pose.

With 21 credits this semester it’ll be possible to graduate this Fall. That’s my current plan. No looking back. Next thing, here I come.

Now what? (audio)

Man, new Facebook wannabe site Zurker must really burn the Diaspora guys. Sorry to rub it in. That Zurker has made any waves whatsoever is a sign that we’re deeply desperate for a replacement for that smug monopoly of a site, Facebook.

Wired recently caught up with Founder Nick Oba and he had this to say about the site’s future:

“Given the support we have, I’d have to intentionally drive this project into a tree for it not to succeed.”

First of all, Zurker is based on the idea of member ownership. That right there could have been a small revolution worthy of attention, except that Founder Nick Oba opted to go with a pyramid scheme, just to make sure that the site wouldn’t miss the tree as it speeds down the mountain. Members get “vShares”, which are supposed to be virtual shares in the site, for recruiting new members. Technically, it’s not quite a pyramid, since you don’t get a share of what your recruits earn, but close enough to produce the same gag reflex. To be fair, social shopping sites have been doing this MLM-like strategy for years now, and it’s totally mainstream these days.

If you go to the Terms of Service on Zurker, here’s what you find (as of 5/21 when I last looked):

vShares are not shares, or stock. vShares are an agreement between the user and the OPERATORS that the user shall qualify for equity. As such, vShares cannot, technically, be “owned,” and the agreement between the user and the OPERATORS may be revoked in case of intolerable abuse by the user; in other words, vShares shall be forfeited in case the user’s account is closed.

vShares records shall be maintained by the OPERATORS until the establishment of an operating entity which apportions equity to all holders of vShares.

TL;DR — vShares are an undefined agreement that Zurker can terminate at will. Some undefined amount of “equity” may be given to vShare holders if we ever establish a company to do that sort of thing.

What do you get for climbing to the top of this pyramid? A whole lot of promises of rainbows and ponies. Wired did some digging on the business history of Founder Nick Oba, and published an article entitled Be wary of cooperative social network Zurker. You must judge for yourself whether there’s reason be wary, once you get an invite. In case the referrals aren’t enough of an opportunity for you to acquire vShares, you can purchase them in bundles, for up to $500 USD a pop.

Based on my short one week experiment, I’ve found the site to be poorly designed, spammy in terms of the number of emails I receive weekly, and full of a whole lot of lurkers. I’ve received several “connects” from people I don’t know, some of whom seem to be sort of evangelists for Zurker. I imagine an army of zealots dead-set on maximizing their vShares. They’re dressed up like Avon salespeople and knocking on my door. No… Noooo! This ironically is exactly the kind of thing Facebook seems to be pretty good at avoiding. Today I went to delete my account. I’m tired of the spam, and fairly confident that this site isn’t worth my time. This could be a case of paranoia, but there doesn’t seem to be a way, or at least, an intuitive way to delete or disable your account. So much for freedom. [EDIT: I found a small type link on the bottom of the settings page, but it took a while.]

On the heels of my last post, How the Cloud Broke Open Source, this post felt relevant. We need real open alternatives to cloud apps like Facebook. I don’t mean hosted open source. I don’t mean a better WordPress. I don’t quite know what I mean, but I know I don’t mean Zurker. I think the future has yet to be invented, but, I’ve got some ideas, and I am sure some of you do, too. Have some opinions? I appreciate comments.

This could be a rather deep topic to broach, so I’ll cut to the point. The cloud broke open source. This is how.

I’ll always be proud of my years in the dotcom world. I worked on internet telephony years before Skype was even an NDA in the hands of a venture capitalist, and I revelled in the increasing breadth and scope of the engineering that was possible as the 90′s became the 21st century. At first, open source thrived on the web, and to be fair, it still does. The Apache server for example, has always been a foundation of the web. However, at some point, starting with email, the “cloud” started to reach the complexity of desktop software, beyond server software, and without the community behind it to push for open source solutions. At first, “software as a service” was an isolated niche, largely integrating with the existing desktop market, but then things changed.

Gmail is the classic example — a good place to start. The fact that gmail offered free distributed (any computer) email with search and spam or virus protection as good as any desktop application drew people to it. They started to abandon their email clients, or in some cases, running their own email servers. Why waste effort and resources on something that’s offered for free? Enterprises are buying in too, paying for the privilege. By now even the most novice internet users know that cloud companies sell our “anonymous” data to marketers and make a fortune doing it. This is the steep payment for all of that “free” technology — our privacy. While privacy, or “data ownership” is the most popular debate around cloud services, more urgent dangers loom.

Nobody ever asked me, “do you think Google will release the source code for gmail?” The answer would have been too obvious — an emphatic “hells no!” This same logic can be applied to any of the cloud companies and services that have become a fixture in our personal (and professional) computing experiences. While it was once possible for open source developers to create applications that were competitive with closed source commercial applications, that opportunity has shrivelled. There is no skunkworks open source gmail. No open source ad-free Facebook. No twitter with code available for download.

Why? There’s no technical reason that the cloud should have broken open source. True, there are open source web applications aplenty. Ones that you can run yourself, or even host on a rented server. However, it all comes down to the tubes. Big cloud providers sink lots of dough into server and network infrastructure to be able to scale applications, and they have a dedicated staff to keep those applications running smoothly. While individual customer service might be close to non-existent for many cloud apps, the fact is that they’re generally reliable, and sell the user a perceived, if not actual service level agreement. This is the part businesses love, as they not only are free from the pitfalls of infrastructure management, but they have an entity to shoulder responsibility for any service failure and the resulting damage.

If I wanted to launch an open source cloud service — say for example, an open source Facebook. Yes, I consider Facebook to be a cloud app, even though social networking didn’t really exist on the desktop until file sharing. As the failed Diaspora project made clear, even having money isn’t enough. You need a large investment in infrastructure engineering and customer support. The barrier to entry has gone through the roof as the challenge has escalated from a single user experience to simultaneously servicing millions of users. Open source made community front and center in technology — not only software, but has simply hit a rather large and painful brick wall with the cloud takeover.

Perhaps the worst offense against open source is the innocuous and seemingly empowering API. You can combine your google docs with Tropo and Amazon.com to create an app that texts you when you’ve mentioned a book that happens to be on sale at Amazon (with prime shipping, even). Oh, isn’t it a wonderful world? Except — try doing that with open source. Good luck. The app you write which uses the API might be open source, but the underlying power and functionality behind that API isn’t. You don’t own the stuff that makes your app work, just the superficial framework. Sugar-coated with useful data, developers hook into closed source APIs and databases to do all sorts of amazeball things.

Some of you will appreciate the irony. IBM and Google pushed along technologies as an alternative to the closed Windows platform. They pushed things to the cloud, and now the cloud is protected behind big shiny gates. No put intended. Is there a silver lining? The tools for the open source web do not exist, yet the necessary components are more or less there. I will be keeping my eyes open for signs of the open source web that I suppose must eventually materialize, like a phoenix from the ashes.

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iGEM

Those are some Hunter iGEM team members with Sung Won Lim, one of our mentors, over at Genspace, a community lab I’m a member of. Everybody’s favorite bacterial computing project is getting off the ground. We’ve received a dozen student applications and expect a few more. Our team is absolutely wonderful, with a great diversity in experience and background. We have several amazing advisors with backgrounds in evolutionary, molecular, cell, and systems biology, molecular modeling, and synthetic biology. We’re still looking for sponsors, but are off to a good start in terms of funding with backing from Hunter College and NIH via the QuBi program, (potentially) University of Pittsburgh, and (potentially) NYU.

Employment

So excited about my new research position! Through September, my job title (full time over the summer) will be “Health Sciences Fellow in the Department of Computational and Systems Biology in the School of Medicine at the University of Pittsburgh”. I’ll be blending some of what I do on the job with my iGEM project, as part of our goal is to build software related to synthetic biology and there is some overlap with molecular modeling. Primarily I’ll be working on the next generation version of RuleBender rule-based molecular modeling software. Molecular modeling is important in biology for understanding the inner workings of complex systems and devleoping drugs and therapies for things like cancer. Technically I’m still a research assistant in the Treespace group at Lehman, but haven’t had much to work on since I joined. I’m hoping I can work out a joint project between Lehman and Dr. Qiu’s lab at Hunter.

Hackery

A bunch of us Hack Manhattan members had a blast hosting a booth at Westport Mini Maker Faire this past weekend. We had EEG brain pong, which a mother let her baby play. We taught people the basics of opening locks without keys (while reading their brain waves!). We even had our own low cost 3D printer design up and running, with plastic “HM” keychains to give to the kids, who loved them. So many smiling people. Westport is quite a beautiful little town.  We also made friends with lots of talented CT based hackers and hackerspaces. See more photos here.

That’s all I’ve got for now. Can’t wait to see what May brings. I have a few things on my wishlist…

Here’s a screenshot of an abstract simulation of an experiment we’re (iGEM team) working on to create a working hash function using XOR-like bacterial logic gates. My python code is here (you’ll need to install pygame to run it). The red/green bacterial colonies are the output and the blue numbers are the inputs. They represent a quorum-sensing molecule from top down and NaCl from the left to right. The output of each bacteria colony is passed as an input to the one below. XOR means exclusive or, so we only get green (1) if ONLY one input is true (1).

I’m enjoying participating at the Hunter Evolutionary Bioniformatics lab, the NYU bioinformatics lab, and the Lehman Treespace group, though I’ve got plenty of catch-up work to do for all of them now that iGEM has started up. Funny how starting a major interdisciplinary research project takes a lot of time. Who’d have thunk it? I’ve also been hanging out a bit at Genspace where I just finished getting my safety orientation, and of course, Hack Manhattan, which I’m afraid I’ve been neglecting as well. God I love those guys (and gals), though. Oh, right, there’s classes, too. Organic chemistry is fascinating, but a handful!

The other day I walked to school. Straight down Lexington Ave. Took me about 45 minutes — not bad. The train in took 15 minutes today. All in all, a vast transportation improvement over East Williamsburg. The apartment and housemates are lovely, too. With Costco just down the street, I look forward to stowing away 500 packs of random things like dried vegetables so I can jump on this whole zombie apocalypse preparedness bandwagon. You know, just in case something goes horribly wrong in the lab and all hell breaks loose.

Happy almost-summer!