Category Archives: Technology

Why not give (productivity) software this year!

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pro·duc·tiv·i·ty  (prdk-tv-t, prdk-)

n.

1. The quality of being productive.
2. Economics The rate at which goods or services are produced especially output per unit of labor.
3. Ecology The rate at which radiant energy is used by producers to form organic substances as food for consumers.

Why not give yourself or a love one access to well design software? With the new years usually comes the time to take resolution(s). And like most they are forgotten a few weeks later.  This is because, we human being, get our attention so easily put elsewhere, diverted by what surround us, in particular the consumption media. So, we tend to get into an unproductive state by putting off what must or should be done. Simply stated procrastinating.

pro·cras·ti·nate  (pr-krst-nt, pr-)

v. pro·cras·ti·nat·ed, pro·cras·ti·nat·ing, pro·cras·ti·nates
v.intr.

To put off doing something, especially out of habitual carelessness or laziness.

v.tr.

To postpone or delay needlessly.
It turns out that having tools that you like to use because of its physical design (an iMac, a Mac Book air or even the new Mac Pro!), the feeling it provide when touching it (like a well-made pen or paper notebook) and well design software all help in getting things done. There are many reasons why certain tools, hardware or software give use incentive to be productive over others or make us more productive. The important point is that you have to use them, use them everyday and actually like to do it.
The first rule in being productive is to actually do something. The second rule is for that something to actually be part of a whole that get your projects moving forward. This implicitly means that you can track your projects, the tasks associated with them and the necessary documents (files, e-mail, …). If you hate the software and hardware your are using to do this or they get in the way because they are not well conceive, you will loose interest, loose track of the important stuff and suddenly the not so important stuff become at the forefront of what you are doing.
Here are a few well design software you might want to invest into (some are actually free) and that are available to OSX and iOS:
  • Professional digital document management: DevonThink Pro Office and DevonThink To Go. On the Mac, you have indexing and AI doing automatic filing for you. No need for Tags. Tagging is a good concept but it does not scale and its efficiency certainly breaks down once you have tens of thousands of files.
  • Note taking app: Evernote (free) or NoteBook. I also find Apple Notes useful since it is always with me on my Mac, iPhone and iPad.
  • Task manager: Wunderlist (free – perfect for student and much better than Apple Reminder) or professional grade Cultured Code Things and OmniFocus.
  • MindMapping software: XMind (free) and iThoughts (Nice interface, intuitive to use, my favorite).
  • Project management (for large projects): Merlin and OmniPlan.
  • PDF management and citation software: Papers 2 (stay away from the “new” Papers 3), Sente or Zetero (free).

Some software should also allow you to get stuff done so you do not have to. In that category, I could not live in the digital world without:

  • 1Password: Strong passwords for all for all of your accounts, safely stored using the best encryption scheme. Never loose time again with passwords.
  • SaneBox: Made me realize that over 40% of my incoming e-mails are non actionable. SaneBox get them out of the way automatically for me. I never thought I would say this (I work with e-mail since 1991!!!), but 5$/month well spent. Work with IMAP, Exchange, iCloud, GMAIL.
  • MacUpdate Desktop: Unless you get all of your software from the Apple Store on OSX, you need to track your software and keep them up to date. MacUpdate does this for you very efficiently. Run it once a month, no sweat.
  • Alfred: Spotlight on steroid!
Merry Xmas!

Cultured Code Things 3 on the way for 2014!

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The team at Cultured Code has announced on their blog that they have reached 1 million copies of Things  sold. In the same blog post, they let us know that version 3 of Things will be coming in 2014. Hopefully it will not know that same fate as the cloud sync version of Things which took over two years after the first announcement…

Attachment-1

Things is powerful task manager. It comes with a simple and efficient interface and is fully scriptable (Apple Script). I have been using Things since its very first beta release. Certainly look forward to V3.

An hour, 10$ and a smartphone = 175x digital microscope

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This is a very nice weekend project either for yourself or with kids! As a bonus, this will let you performed digital capture (photo 😉 ) of your observations at no extra cost (other than assuming you do have a smartphone with an integrated camera)

Instructions from PetaPixel (video) and Instructables (step by step).

 

What is going on at Mekentosj with Papers 3?

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Having a PDF management system, which allows in-app citation (e.g. WORD, Pages, Mellel, …), is a necessity for scientists and researchers. On OSX, we have the chance of having the choice between extremely well-design and efficient applications such as Sente, Mendeley and yes, Papers (there are of course free options, as always it depends how much time you want to spend working with your tools relative to working on your tools!).

 In the past I have used Endnote, Zotero, Sente and finally settled for Papers starting at version 2.0.8 for its extremely well thought-of citation mechanisms, PF editing options and nice interface. A review is available here in the e-office series.

Zoom to the latest version (still a beta) of Papers. Yes the interface changed quite a lot, both on OSX and iOS. Mekentosj seems to have adopted the design element of iOS 7 as a reference across the board. Quite frankly, the only thing I do not like in iOS 7 is the color scheme used for certain icons. Otherwise, I like it very much: it is clean, simple, introduced great new stuffs and does not get in the way. 

Below are the screen captures for iOS version of Papers and Papers3. 

Papers-iOS

Papers3-iOS

So, you say great this guy love Papers 3. Not at all. Design change you can get use to it (assuming it is for the better) but key missing feature is a problem.

Papers 3 allow syncing via DropBox or import/export of the whole library…Gone is the great WiFi sync of the previous version. Why it is this important? My library is large, closing in 5 Gb. I do not want to put that on DropBox (or on any servers for that matter) nor do I need to have all of that in the Cloud. The DropxBox options look interesting for a small library but for large libraries I am not convince and I feel it is unnecessary to pay for cloud storage space to store my library (this is why I do not like Mendeley for example). Even my library at close to 5 Gb is not that large and only contains over 4000 entries.

When I ask Mekentosj about it, I received the following from the support staff:

Hi there

Thank you for your feedback regarding this. I’m afraid that Dropbox is the only solution at the moment. However, we hope to include a possibility to sync via Wi-Fi in some point as well. However, depending on the technical aspects and Papers release cycle, it’s hard to know yet when that’s going to happen, so please be patient

So it might or might not happen in the future. For now, I would think that this is a big deal for users with large libraries. I reverted back to Papers2 like a number of my colleagues.

Overall, very disappointing first contact with Papers 3

 

NOTE: Academic workflow on Mac also has a coverage of Papers 3 which describes other important issues

OSX 10.9 (Mavericks) is available and free!

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Wired is running an interesting piece about the latest operating system from Apple. In part past, Apple provided free or very low cost upgrade for its “minor” version of OSX but paying upgrade for significant new version. 10.9 is a significant upgrade but will be free: Apple Just Ended the Era of Paid Operating Systems | Wired Business | Wired.com.

In a related news, iWork (Numbers, Keynote and Page) will be free with each new Apple computing devices, Mac or iDevices! Office productivity and MS Office compatibility out of the box. That should be interesting…

Big Data, Scarce Data: Which One Fits Medicine?

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IMG_1139

While visiting CERN last spring, there was a catch phrase used during the visit that stick in my mind. For the ATLAS detector, at the heart of one of the 4 main experiments at CERN and also one of the experiment that found experimental evidence for the Higgs boson (or a Higgs boson…), the interesting data were the equivalent of a 100 megapixels camera taking 400 photos per seconds (or maybe the other way around, but it does not change the shear scale of things)!

This amount of data is after all kinds of real-time software and hardware processing because the raw data during normal operation (read beam on condition) is close to 1 PetaBytes/sec (MB, GB=1000MB, TB=1000GB and finally PB=1000TB)…and this is only for ATLAS. In fact everything about the Large Hadron Collider (LHC) is big, from cost, to equipment, to human resources and data generated. Nature had an interesting article about how the data are handle and distributed worldwide among the collaborators.

IMG_1150

Now what about medicine? We hear a lot about big data in biological sciences and medicine. The main problem, at least in medicine in my opinion, is not that there is too much data for the researchers and physicians but rather the other way around. Database for clinical trials conducted at various levels (from internal trials at individual hospitals to more global trials) are not all, or at all(!), compatible with each other. Furthermore, numerous database tends to be incomplete not by design but simply from the difficulty of filling and ensuring data integrity. While big data also sounds great for personalize medicine, personalize medicine by definition means low numbers of very specific medical conditions. Overall, we are unfortunately at this point in time in a scarce data mode.

The next big step for big data in medicine is a revolution with regards to database management, sharing and analysis. And yes personalize medicine will likely mean bigger research consortium and more sharing of data. There is a lot to learn from the particle physics community and initiative like the LHC. I do hope that those big data grant programs we are seeing in our country is to address that in priority. Until then, we will remain with incomplete or scarce data in medicine.