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Tag: productivity

Introducing TranscribeSharp

I've previously recounted how I was (am) unsatisfied with ExpressScribe for controlling audio playback for transcribing interviews. Because the basic functionality of the program is so straightforward (using global hotkeys to control audio playback), I was disappointed that there was no free, open-source alternative to ExpressScribe. So I'm making one.

The TranscribeSharp UI
The TranscribeSharp UI is essentially identical to the PracticeSharp UI in this preview release. Transcription-focused changes to the UI are planned.

TranscribeSharp is a program that will let you control the playback for audio files using hotkeys while you transcribe the file in another program (e.g. Microsoft Word or LibreOffice Writer). You can slow down, speed up, fast forward, rewind, pause, etc. the audio using you keyboard without ever leaving the program you are transcribing with.

The Hotkey Settings menu
The Hotkey Settings menu can be used to change between two predefined sets of hotkeys.

TranscribeSharp is in large part based on PracticeSharp by Yuval Naveh with addition of the LowLevelHooks library by Curtis Rutland. I do not consider myself a skilled programmer, and TranscribeSharp is in some sense just these two pieces of software smashed together. Without PracticeSharp and LowLevelHooks, TranscribeSharp would not be possible.

Right now, this is just a preview release. There are a few bugs, but it is a functional software solution. I wrote this to use for transcribing interviews for my dissertation, but I figured that other people may be interested in using it as well. This is a very low priority project for me, though, so please understand that. I do have a list of features that I would like to eventually add (e.g. the ability to customize the hotkeys, video playpack, an installer, and a different UI), but I have no timeline for implementing these.

TranscribeSharp is written in C# using Visual Studio 2013 and licensed under the LGPL. The full source code is available at BitBucket. If anyone is interested in helping out with bug fixes or implementing new features, just get in contact with me - I am very interested in not working on this project alone. (This was also my first time really using Git, so in future releases I intend on re-structuring the way I use the dependencies.)

To use the program, just unzip the file below and run TranscribeSharp.exe. You'll need the .NET Framework (at least version 4) installed to use it. The program should work on Windows 7 and 8 (maybe more). I hope you find this program useful.

Download TranscribeSharp (Preview) version (zip, 2.6 MB) here


On Elsevier buying Mendeley

[Update: Steve Dennis, a developer for Mendeley, posted a comment explaining a bit more about the data collection and privacy concerns some users have with Mendeley Desktop. It adds some pros and cons about the process outlined here.]

Two days ago (2013-04-08) Elsevier (the academic publishing company that is the subject of some controversy) bought Mendeley (the reference manager and a tool often mentioned when discussing 'open' research). The Mendeley Blog does a quick Q&A covering what changes will take place (they take the position that this will be better for everyone), while the folks over at The Chronicle examine the sale with a slightly more critical lens. Some accounts I follow on Twitter began using the hashtag #mendelete, taking an even more critical stance on the sale. (Someone has even made a guide to exporting data from and then deleting one's Mendeley account - useful, even if just for the exporting data portion.)

While it remains to be seen what changes will, in fact, take place, the simple fact remains that Mendeley is not open source and remains controlled by a company that does not have my (and your) best interests in mind. The most important thing for Elsevier is making money, and, for now, keeping Mendeley operating serves this goal. However, my work is too important to rely on a tool that somebody else controls. (I did a pretty thorough post on my views about this after the discontinuation of Google Reader.)

Now, Mendeley advertises itself as both a reference manager (think iTunes for PDFs) and a social network. This social network aspect has generated a lot of data, and many researchers seem to find it useful. Consequently, Mendeley has integrated their web services and their desktop client so that a single account is required to use both. Yes, an account is required to use the desktop software that would work perfectly well without an online account. Sure, it is enhanced by internet connectivity, but an internet connection is not required to organize my documents.

The login window that appears when Mendeley first launches.
When Mendeley first launches, there is no option to skip logging in.

But, an account is not really required. With a teeny bit of work, the Mendeley desktop software can be configured to work without a Mendeley account. This solution comes from the Mendeley support website, and is used to help people launch Mendeley when there are issues with the software and/or accounts. It is a 'feature' for support, but is certainly not something they advertise. The trick is to add --setting General_FirstRun:false (with two dashes, an underscore, and a colon) as an argument to the program when it launches. I'm doing this on Windows, but as Mendeley is cross-platform, it should ostensibly work on OS X and Linux, too. (Let me know in the comments if it does or doesn't work.)

To add this argument, right click the shortcut for Mendeley (e.g. the one on your desktop) and select properties. Then, add it to the box labeled "Target" outside of the quotation marks. Check out the image below.

Mendeley Desktop Properties window with the Target field circled
Notice the argument is outside the quotation mark and uses two dashes (-- not -).

After clicking Apply, you may need to grant Administrator approval for the changes to be saved, depending on your UAC settings. Adding this to the launcher skips the initial window that asks for your account information allowing you to use the offline features of Mendeley in peace. (You can add an account later by choosing "Tools" followed by "Options".)

Now, this option works with at least Mendeley Desktop 1.8.4, but there are no guarantees about 1.8.5 retaining this same feature. (Though there are many uses for this ability in a support context and removing it would be silly.) I feel somewhat assuaged knowing that I can use Mendeley on my computer whenever, wherever. Moreover, if I ever need to install Mendeley and their servers are unavailable, I can still use it.

I'm not Men-deleting my account. Not yet, at least. I'm still holding out hope that the program will be made open-source, assuaging even more of my concerns. There may still yet be hope according to something I saw from William Gunn, Mendeley's Head of Academic Outreach:

A conversation on Twitter between @TheDougW, @mrgunn, and @MendeleySupport.
Apparently open sourcing Mendeley is still being talked about.

So, open source is still being talked about, and the API is remaining open. These are promising signs. For the meantime, at least, I'm going to check out using Zotero in addition to Mendeley. I've been hearing some good things about Zotero, and it never hurts to have options. As the saying goes, "Two is one, one is none."


On submission and rejection

Rome wasn't built in a day, nor are good manuscripts published in one. I've heard similar comments for some time, but they don't really ease the sinking feeling when an email containing the tactful "unfortunately..." that often precedes the 'we are not publishing your manuscript'. So it goes.

Swallow hard. My CV has been once again updated ('under review' becoming 'in preparation'), and time to get back to work on this project. Bigger and better (guided by the reviews' comments). Meetings, coding, and reading. Things to keep me from getting bored.

On a similar note, I got back in touch with a professor from last semester to talk about collaborating and expanding a project I did for class last semester. This happened within a half hour of getting the aforementioned email.

When it rains it pours. Hopefully this will water the seeds.

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Quite a few minor issues today

I've been doing a lot of writing in Microsoft Word lately (there are others working on the same document and LibreOffice Writer can't seem to get it right), so I've been living in Windows-world. Yesterday I needed to access an R package that is UNIX-only apparently (heR.Misc - really? No Windows binaries?) and was greeted by Scientific Linux with some updates to take care of. Most of the updates installed fine, but five did not. The five that did not were all related to Qpid (packages like qpid-cpp-client). These could not be installed because yum could not resolve some dependency issues. Apparently the issue was that these updates were related in some way to the matahari package, which was deprecated by Red Hat (according to this forum post at least). A quick sudo yum remove matahari in the terminal and the updates installed correctly.

I figured while I was updating software that I would try to get an Aero Snap-like feature working in Linux.  As much as I like the stability of Linux, I dislike the lack of some should-be-standard features in GNOME. In Windows 7, there are some great features like Aero Snap (automatically half-maximize windows) and windows grouped on the taskbar. CompizFusion can... somewhat perform these features, but not with the polish and consistency that I've come to expect.

I just care about my computer supporting my productivity, and I am therefore not attached to any particular window environment. KDE 4 seems to have implemented some of these features without the use of add-ons, so I figured that I would give it a try. However, installing KDE using YUM wasn't immediately obvious. Searching for "kde" resulted in tons of packages, but none seemed to be a wrapper for the entire environment. Eventually I went to the command line and executed (as root):

yum groupinstall "KDE desktop"

However, I should have realized that Scientific Linux doesn't have the latest, greatest packages. The KDE that was installed was version 4.3 and... didn't do what I wanted it to. I promptly switched back to GNOME and started playing around with CompizFusion.

Long story short, I got frustrated and gave up for the time being. I am determined to get this to work, but I don't have the time to devote to it right this second. I think this is where things went wrong: I wanted to uninstall KDE and did

yum groupremove "KDE desktop"

which uninstalled all KDE-related packages and not just the ones that had been installed above (I had previously installed some packages like kdegraphics which contains Okular (a great PDF reader)). While I would like to figure out how to remove an entire group  except for certain packages, that's something to solve later. No big deal, I didn't use them much and could always add them back later. I rebooted my computer to complete some updates and...

No internet when it came back. The GNOME panel icon was just... gone. Now, my first instinct was to search the internet for related issues. I was able to get online by plugging in an ethernet cable and running, as root,

ifconfig eth0 up
dhclient eth0

This gave me wired internet, though Yum Extender didn't want to believe it had internet. I ended up having to run from the terminal

yumex --root

to be able to install packages.

Most of the resources I found related to Ubuntu which can be rather different from Scientific Linux/CentOS/RHEL. I tried to see if the network manager was still installed by running

[Doug@FLASHMAN-SL ~]$ service network-manager status
network-manager: unrecognized service

Seems like a problem... except the network manager is not called network-manager in Scientific Linux. It is actually called NetworkManager.

[Doug@FLASHMAN-SL ~]$ service NetworkManager status
NetworkManager (pid  2077) is running...

I spent way too long reinstalling NetworkManager when that was never my issue. What it turned out to be was the program nm-applet was missing (uninstalled at some point), and I just needed to (re)install the package NetworkManager-gnome.

That was a headache that was mostly my fault, but the lack of solid documentation (and vague search terms like "gnome internet icon missing") made this difficult to figure out. Maybe putting all of these search terms in one place will help other people.

As an aside, my school (UF) now offers Red Hat Enterprise Linux to students... and I am toying with the idea of switching from Scientific Linux to RHEL. However, UF is running RHEL 6.1 and I'm running SL 6.2, and I would prefer to not do a clean install. Unsurprisingly, Red Hat does not support cross-grading (I asked), and I don't want to fiddle with a simultaneous cross/downgrade. Though I must say, the support would be nice for situations like this...

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