Lecturing with google Slides (Post 3: academia and chromebooks)

I'm sorry for the delay in the next instalment for my series on science and academic uses of google chromebooks. A close friend of mine passed away, and that's taken up most of my thought processes for the last week or so. Thank you very much for the response to the last post on google docs and paperpile, it was great to hear from a bunch of you via the comments, google+, and the chromeos sub-reddit. In particular, I'd like to thank the person who pointed me towards GetDataJoy as a method of coding in Python on the chromebook. I'll be doing a full write-up of that in the future. However, today's post is fairly simple and will discuss the use of google Slides for lecturing in the class room.

Preparing lectures

If you are familiar with Powerpoint and the many derivatives, then there's not really a whole lot to say about google Slides. It is simple to use for creating clean slides, with enough animations and transitions to keep the audience happy/pissed-off. I used to be an OpenOffice Impress user for all my lecturing and conference presentations, but I have been converted to google Slides for a number of reasons.

Firstly, there are helpful guides for placement of objects when you are arranging the slides. These are simple red lines which, intelligently, appear when you drag or re-size an object and let you know if you are centred or aligned with the other objects on the page.

Secondly, things just look better than compared with OpenOffice. I don't know if this is just because it's new, but I genuinely believe that the fonts and shapes are rendered better in Slides. The available transitions look great when used in moderation, although I tend to only use the 'cube' transition for section changes and leave transitions turned off for every other slide.

Thirdly, and this isn't something that I use particularly often, but I like the ability to turn up at a lecture theatre empty handed, safe in the knowledge that I can use the browser on the theatre's computer to give me my slides. Should I suffer a catastrophic loss of my laptop and/or chromebook, then this will be very useful in the future!

Student feedback and collaboration

A theme that runs through my love of using google chromebooks for my academic life is the ability to collaborate with other users. When it comes to lectures, this acts more as a feedback channel for students. Students, who opt-in, are given sharing access to my lecture slides and are then allowed to view the content in their own time.

Figure 1. For better or worse, students can add comments

If they have any questions about specific slides, they can leave comments on the side bar. At the next lecture, I am able to pull up the previous lecture's slides and work through any comments that have been left before continuing with the material. These comments also serve to help me improve the lectures for the next year's cohort. Let's call it formative assessment of my lecturing.

I am currently working on a series of lectures with another colleague, and by using Slides, we are able to directly work on the material together. This allows us to focus on what parts of the course we are giving to the students, and lowers the risk of missing parts out because we thought the other person had it covered.

Figure 2: Planning content for the students to suit all parties

Keeping the screen turned on!

During the first lecture which I presented with my chromebook, I came across a really annoying feature: chromebooks don't have an in-built feature to keep the screen on, nor do they have the ability to change the amount of time it would allow before turning off the screen. I would spend 10-15 minutes lecturing via Slides before heading over to the whiteboard to expand on an item, or work through an example. I'd get half way through the example and the chromebook would be in sleep mode, turning off the HDMI output and all. It would then take a small amount of time to come back to full working mode. Our University uses eduroam for WiFi and this is the main slow point when working on the cloud (and is currently causing me annoyance by dropping out while typing this!).

Figure 3: Keep awake button on
the button bar.

I found, through an internet search, that I was not alone in feeling this annoyance. I found a plug-in for chrome which has three settings: Default, Screen Always On, and Never Sleep. I would advise that people who want to use their chromebook to install this plug-in immediately. However, don't do as I did and leave it on "Never Sleep" when they put their chromebook back in their bag for travelling home. That didn't end well. 

Always leave them wanting more

As ever, there are things missing from Slides that I'd expect from a presentation package. Particularly, I would love to have a proper slide organiser viewpoint. Currently, slides are presented down the left hand side of the screen and are able to be organised here. This gets pretty awkward with 20+ slides that need to be re-arranged.

After writing about how much I loved Paperpile, I would love for paperpile to be available for Slides. However, this would require Slides to have Add-On's in the same way that Docs does. I find it strange that they haven't made Slides as extensible as Docs in this respect. 

Until next time

That's about all I want to say at the moment about Slides. It's a fairly basic, but very useful, addition to the google Office environment. I think I'll write about GetDataJoy in my next article, but I am open to suggestions. 

Oh! Before I go, does anyone else notice their chromebook gets really sluggish if they don't restart it after 2-3 days, crashing individual tabs, and ultimately freezing? I thought that a selling point of a chromebook was that it wouldn't do this. I'm currently using an Acer CB3-111, and trying to work out if it is on its way out and I need an upgrade (my model only has 2GB RAM), or if this is a problem that will be persistent.

Academia and chromebooks Part 2: Collaborative writing with google Docs and Paperpile

Thank you for the response to the previous post about using Google Sheets to organise a lab group. I really didn't expect to have such a high readership or engagement on the first post! That has given me motivation to carry on the series. Today's topic is Google Docs and Paperpile for collaborative writing.

Google docs for collaborative writing

There are many reasons as to why I've made the switch to Google docs for my academic writing (including the basic "I have a chromebook and it doesn't run Microsoft Word").  The main reason being that most academic writing is collaborative and therefore Google Docs is a great solution to the revision tracking and management problem.

If you work as a researcher in a University you will be aware of the high number of collaborative documents that have to be written.  I have grown very tired of the rigmarole of sending Word documents between the writers, all using different referencing packages, different styles for naming the file after revisions, and of course, different proficiencies at editing the most up to date version of the document. If there is an easy content management system, such as github, for Word documents, I've yet to see it. Google docs allows a single document to be edited by all writers at any one moment, with changes easily visible and revisions tracked.

Figure 1: Adding comments to student reports without writing it for them.

When I have a student who has to write a report, I have them start a new Google Docs document and immediately share it with my email address. That way I can keep an eye on their progress as they write it, without having to wait for them to send the first of many Word files in the early hours of the morning, which get hidden amongst all the other spam that arrives through the night. This might sound a bit 'Big Brother', however, in this case I have found that students work more on their reports if they are aware that I am keeping an eye on it.

I have to be careful to avoid writing reports for my students, and therefore, when I have a shared document with the student, I have the sharing properties set to "Can view and comment" only. With comments, I can give the student immediate feedback on their writing (shown in figure 1), and they have the option to respond, accept or (if they are bolshie), decline.

Paperpile: A reference manager for Google chrome and Docs

For a word processor to be useful for academic writing, there needs to be an easy way to incorporate a bibliography for citing other work. Over the years I have tried many different programs, from Endnote to Mendeley via Zotero, with the Mendeley being my favourite for OpenOffice work. Unfortunately, Mendeley doesn't have a Google Docs extension and therefore I had to find another option.

Figure 2: Adding a web reference to Paperpile with the Google chrome extension.

That's when I found Paperpile. This is an on-line reference manager that operates in much the same way as Mendeley. There are three parts to paperpile, the website and the extension (shown in Figure 2) in Google chrome (it is currently only available for chrome), and the Google Doc add-on. 

The Paperpile website acts as the reference manager portion of Paperpile. You sign in with your Google account, tell it where you want to store PDFs on your drive and away you go. You can manually enter information about papers, but the real power comes from the extension.  When you come across a paper that you would like to have in your reference library, you simply press the button on your tool-bar and the document is ripped of its metadata, entered into your Paperpile library and, if available, the PDF file stored to a folder in your Google drive. 

Over the years I have amassed a large reference library (and corresponding pdf folder). Paperpile had no issues when importing this in to its own library, it even has the ability to import from Mendeley while retaining any sub-folders and organisation you had.

Figure 3: Citing a document with paperpile

It is easy to cite documents using paperpile through the Google Doc add-on (shown in Figure 3), and the references are automatically listed at the end of the document (with all the standard Harvard, Chicago, etc formats that you'd expect).  The paperpile add-on also allows you to search for papers online which you don't have in your library and cite them (behind the scenes, paperpile adds the ones you use to your library).

Another great thing about paperpile is its Shared Folders. I can create a folder for each research project in my lab to act as a repository for the researchers working in that field, then they have immediate access. This is much easier than sending them email, after email, of PDFs to read, and allows them to cite the papers immediately in their documents.

I have been very impressed with Paperpile and have purchased enough licenses for my lab-group members to use it in their work. Student's have a habit of neglecting their referencing when writing reports, but through the use of google-docs and Paperpile, I have managed to improve their grades in this area. 

Imperfections: Areas that need improving

Despite giving a glowing, google-fan-boy, review of Google Docs here and to my colleagues, there are a number of imperfections and improvements that I would like to see. Firstly, and this is a really strange omission on Google Doc's part is the absence of captions for figures inside a google Document. While writing this post in Google Blogger, I can add an image and then give it a caption which is formatted and appears under the image. This doesn't, for some reason, exist in google Docs despite the common interface.

Another omission is the ability to number headings and produce a proper table of contents. Currently, I am using a third party add-on to number my headings and subheadings, which works OK except that the table of contents doesn't show the corresponding page numbers. If anyone knows of a third party add-on that does this, please let me know. 

Finally, the only criticism I have of Paperpile is the lack of an offline mode. I have seen this addressed by Paperpile, and that it is due to the design of the back-end of the database. If an offline mode was available (alongside OpenOffice and Word plugins), I could definitely see Paperpile overtaking Mendeley as the reference manager of choice. 

Next article

Thanks for reading, I'm sorry that it turned out to be quite a long post. Perhaps I should have split this in to one post for google docs, and one for paperpile. The next post will be about preparing lectures with google Slides.

Science Labs and Teaching with chromebooks (Part 1)

A new series of posts for 2016

I've decided to start a series of blog posts about my day to day life at the University of the West of Scotland where I am Research Theme Leader for Ultrasound Imaging. The main focus of these posts will be the use of a chromebook for Academic and scientific work. The reasoning behind this is to disprove the, false, notion that chromebooks are merely devices for browsing the internet and social networking.

I currently use an Acer CB11 chromebook, it's not the most flashy of devices but it does most of everything that I require. I dabbled with crouton for a few weeks to get a full linux desktop on the chromebook, however, I didn't use it enough to justify the space it took up and therefore I powerwashed the device back to the standard chromeOS. These blog posts will try and stick as close to a standard chromebook as possible.

I have a rough idea of the topics that I will cover in upcoming posts (which will start properly after this list!), and I am open to suggestions and comments from readers regarding their use, positive or negative of chromebooks in any academic environment. Upcoming topics include:

• Running a lab-group with Google Sheets 
• Academic writing with Google Docs and Paperpile
• Presenting lectures with Google Slides
• Project planning with Gantt

Running a lab-group with Google Sheets 

I currently run a small research group which focusses on Ultrasound Imaging, and developing high resolution probes for biomedical imaging and NDT measurements. I currently have 2 PhD students and 2 undergraduates working for me. In the near future I am recruiting 3 post-docs, and will have 4 visiting students working in the laboratory. Each person working in my group has their own research project which they work on autonomously, with overlap to other projects to install a group dynamic and teamwork.

I was looking for a simple method of keeping track on the research and work carried out in the lab-spaces, preferably with a method to produce reports or summaries of outputs and issues. In the past I have designed an SQL database with front-end to gather this information, but I found that this took up too much time in the debugging and design stages. Google Sheets provided a simple solution which the lab members have found easy to adjust to.

Figure 1: Google Sheet set-up for lab recording

Instead, a google Sheet was created with five, self explanatory columns (Figure 1) and a form is used as the front-end (shown in figure 2) All lab members are advised to keep the link as a bookmark in their browsers. At the end of each day spent in the lab, the user visits the form and enters their data. This has been designed to take no more than 20 seconds, and is to be used as a shorthand summary of their formal lab-books. I have designed the form such that the member selects their name from a drop-down list, this reduces their data-entry time and formalises their name as the identifier for their data. 

Figure 2: Form presented to the user

Once their content is submitted, the spreadsheet is automatically populated. Since the spreadsheet is hosted by google-docs, I have access to this data anywhere that I have internet access (via the google Sheets app on Android, or my chromebook).

However, the main benefit of using this method is the ability to have a worksheet for each member of the lab inside the google Sheets file. In each worksheet, a pivot table is used to create a live report of their work. Some of my lab members have to fill out a monthly report for their Visa requirements, and the ability to send them a monthly PDF of their pivot worksheet as a lab progress report is a real time saver. 

As part of the running of the lab group, I hold weekly meetings with the whole group to keep track of what is happening. Using a chromebook to have immediate access to these pivot tables for each lab member has been very useful for engaging with the quieter members of the group.

Inside the main spreadsheet, I have my own private columns where I can add notes and tags (project names, other supervisors etc) to expand the usefulness of the data. With this supplementary data, I have my own set of pivot tables that allows me to pull out entries relating to a body of work or project (or indeed, time period), allowing me to keep better track of what is happening in my lab group.

This method doesn't use any special software or add-ons (indeed it would work on any computer with access to google docs), and I would recommend it as a free method of logging your lab member's work. The benefit of using a chromebook is the 10 hour battery life for when I am in the lab all day and away from my office, with the spreadsheet available as an offline file for where the WiFi is patchy (hello 1970's architecture!).

In the next post, I'll talk about how I engage with my student's academic writing with Google Docs, and the use of the wonderful Paperpile app as a reference manager and citation tool.

Faith in open source software tested to the limit.

I'm a big supporter of open source software, I've used linux as my main operating system for the last 10 years (if not more). At work, as a scientist, I've made use of the large catalogue of scientific software and tools on offer to Linux users. I've always been a staunch supporter of open source over propriety software, recommending people seek out the alternatives before parting with cash for mainstream solutions.

However, over the last few years I've been noticing an increasing problem that I think needs addressed before there is mainstream adoption of Linux as a desktop solution. Namely: Brilliant software ruined by less than optimal upgrade cycles. More regularly than I would like, I update my system and then find that software that I base my work (and hobby) life on no longer works.

Scilab

Scilab is a mathematical software package. I've used it since I was an undergraduate physics student (graduating in 2005) as an alternative to Matlab. It formed the basis of my PhD thesis work in to signal processing and analysis, and I even delved in to controlling hardware with it's SciCos modules. Now however, I need to find an alternative because, after updating my system, Scilab's push to a new underlying API has been at the expense of being able to plot data on intel hardware!

No longer can I read simple data in and plot graphs. This is the simplest use of Scilab, and one that formed the basis of many images in my thesis and papers. I could understand if it was obscure hardware that the graphical library didn't work with, but seriously, Intel!??!? 

Mendeley

Mendeley is a wonderful tool for sorting out academic papers and keeping a track of citations. In a lot of ways, I would still recommend it. However, today, while trying to make headway in writing a few articles, I have found a very serious bug that makes it all but useless for its task: Mendeley is unable to insert citations in to OpenOffice. 

The developers have known about this bug since April, other updates and bugfixes have been issues, but this seems to be less than urgent from their point of view. From an academic point of view, I am no longer able to keep a dynamically updated bibliography section at the bottom of my paper as I write it. I can't even edit the existing reference list.

JackD

Ah Jack, the godsend for Linux Audio, which worked brilliantly for a good number of ages before some bright spark decided that it should go the same was as Pulse Audio (ugh), and upgrade to JackD2. Without warning, the wonderful multitrack studio software studio Ardour is unable to export audio without disabling all audio plugins (EQ, reverb, compressers etc). Fine if you want to render dull, unmixed studio audio, but that then misses the whole point of what a Studio environment is for.

Why?

It seems that developers of high profile open source software want to be seen to be staying ahead of competition, and by making use of the free nature of the upgrade cycles afforded by open source, rush out these upgrades without any proper testing. "The audience will test it" seems to be the mantra, forgetting that there is a reason that the community should make use of Nightly Builds (new stuff, not tested), and Stable builds (more stable than nightly, but needs more testing), and Release Candidate (stable as fuck, as good as the existing sofware but with new and WORKING features). 

Unfortunately, we are unwittingly being upgraded to Stable builds rather than Release Candidates and these problems arise.

Right, I'm away to find alternatives, until they break too.

A challenge!

My wife just said that the problem with my blog is that I called it Itchy and Irritated, and thus can't write about happy things. I see this as a challenge.

Work has been pretty damn good recently, I've been working on a cell tracking algorithm for tracing the movements of cells under stimulus. It seems to be working pretty well, which is strange since the code below it is very simple. My boss says we may even get a paper out of it, which would be ace as I've only been in the job three months.

Outside of work, life has been enjoyable. This weekend was spent traveling around the UK being paid to play music, to people who were actually listening and singing along. An upshot of the mini-tour is that I may have a split record (on a cassette format) coming out early next year on a proper record label. That would be pretty sweet, but I can't say much more at the moment.

This weekend has a busy schedule ahead. My mother is visiting tomorrow, which is the first family member we'll have had visit us in Dundee. Then, on Saturday I'm playing with the band at The Vale in Glasgow, which we're also recording for a live CD. Sunday will contain a flying visit to Greenock for lunch with the parentals, and then home to Dundee.

Although, do you know what's been irritating me this week? The fact that I've noticed how much FUCKING LOUDER the adverts on E4 are compared to the program I'm watching. That is fucking annoying.

Damn, almost made it. Now, a new episode of Scrubs is on, and that in itself is fucking irritating.

Sales pitch

Today was pretty exciting at work. Well, as I'll explain in a minute, the morning wasn't, but the afternoon was pretty cool. Without going in to much detail, but the device that I've been employed to work on at the university showed its first signs of working today. I recorded lots of videos of the cells doing cool stuff under the influence of the device. Not bad for only two months in the new job.

Why was the morning not exciting? Well, I had to go to a course about a piece of software called LabView. Anyone who has worked closely with me over the last, oh, I don't know, perhaps 8 years now will know that when I want a computer to do something, LabView is second from the bottom (only to a fucking hammer and nails) in my choice to achieve my goal.

For those who haven't had to experience Labview in all it's glory, it's a graphical programming language. You create programs, namely scientific data capture and analysis programs by dragging and dropping Virtual Instruments from a tool box on to your canvas so as to build up a picture of your house with your pet cat outside that you can show to your supervisor so they can see what a clever five year old you really are.

The people who were hosting the class were very much sales persons, with the main 'tutor' getting right on my nerves for a couple of reason. Reason number one, he introduced himself as an engineer who had never really been a fan of computer programming and so Labview was perfect for him since he had no experience of using "C-basic or whatever". Direct Quote. Heya, I've only ever drank coca-cola so I'm going to tell you exactly why it's the best drink out there.

The second reason he irritated me was that he continuously made reference to the fact that in "C-basic" if you were to miss out a semi-colon, you would have to spend hours looking through your code to find the error. Where as with Labview, this doesn't happen since Labview shows you exactly where your mistakes are. Erm, sorry, but anyone who's using a programming language as part of their job would more than likely be using an editor with syntax highlighting, that after compilation would, going by the compiler errors, highlight the offending line of code. Perhaps even give a line number.

Labview on the other hand doesn't even have a zoom out feature so that when your pretty picture, I mean code, gets so large you can't trace what the hell it's actually doing. I asked the presenter why the new version still doesn't have a zoom out feature, to which the answer was "we usually just recommend people buy a bigger monitor".

I could go on all night about this, but I won't. I haven't even mentioned the boasting of "multithreading", which was just a rebranding of the "multi-tasking" introduced in every operating system with the POSIX standard. You did not invent it, you merely made use of the fork functions available on your target platform. I could do that in C, and the program wouldn't need to be restarted every time I want to open a word processor on the same fucking computer.

Thank you, and good night.