Thursday 5 May 2016

What is the molarity of water?

An interesting little question and a fun bit of maths...

The molecular weight of water is: 18.02 g/mol

The density of water is 1 g/ml

Therefore 1 litre of water (1000 ml) would weigh 1000 g

The molarity of something is the number of moles of that thing per 1000 ml volume.

So we have 1000 g of water in 1 litre, and the molecular weight is 18.02 g/mol

Hence mass divided by molecular weight gives us the number of moles, so 1000 / 18.02 = 55.49 moles.

The 1000 g of water is in 1000 ml (1 litre), so the molarity of water is 55.49 M

If you are struggling with moles and molarity, you might find this blog post useful: Why is memorising the molarity formula a bad idea?

You can also test your understanding of the above calculations at:

Monday 25 May 2015

Four really useful exam tips

Recently I asked some colleagues for some revision and exam tips, and this is what we came up with:

1. Do you know where and when the exam is being held?
Sounds obvious, but it is worth checking you know where and when your exam will be held. There is nothing worse than spending weeks (hopefully) revising and then turning up at the wrong time and wrong venue and missing the exam. Also, make sure you set more than one alarm clock if your exam is first thing in the morning, or get a friend or parent to phone you up to make sure you are out of bed and heading to the exam hall. 

2. Try to get plenty of sleep before your exam
Try to get plenty of sleep the night before the exam. Being sleepy during an exam is not good.  Don’t try to boost your alertness with caffeine, and do not pull an ‘all-nighter’ revising the night before the exam. That last-minute ‘cram’ very rarely works. 

3. Think Positive
In an exam, don’t panic, and think positive. If you encounter a question you don’t understand, move on. Don’t sit there dwelling on it; leave it and come back to it later. Be positive. Don’t panic.

4. Don't Dissect!
Do not post-mortem your exam as that will only cause anxiety and distress. Resist the urge to talk to friends about the exam. As soon as the exam has finished, go off for a walk or a treat, and don’t hang around with your classmates that think either they did brilliantly (“that was so easy!”) or who think they have failed (“that paper was impossible”). Resist the urge. 

17 Revision Tips....

Recently I asked some colleagues for some revision tips, and this is what we came up with:

1.  Try answering questions from past papers
Have a look at past papers and try some of the questions. However, don’t fall into the trap of thinking that just because a similar question has come up in recent years, it will be on the next paper, or thinking that as a particular question hasn’t been seen for several years, it must be due to make a return. Examiners are sneaky…..

2.  Don’t become a revision Zombie
Revising for an exam is hard work, but if you work smart and start your preparation early, you will reduce the risk of becoming a Zombie. Try to take breaks, do some exercise that clears the mind and gets the blood pumping to the brain. If you become a revision Zombie, please resist the urge to attack your classmates and eat their brains. If you see a Revision Zombie, RUN!

3.  Your brain is not a sponge - be an active learner
Your brain is not a sponge; it needs to be exercised. If you went to the gym to get some exercise, just standing there looking at the weights or the running machine will not do it. You need to be active; you need to be involved. The same is true of your brain. Just reading your lecture notes won’t do it. You need to be ‘active’. Read the notes, put them down (so you can’t see them), recall the material (re-write or redraw it), and then check it against your original notes. Doing this will strengthen the memory of the material.

4.  Keep your brain alert
Your brain needs food; your brain needs oxygen. If you just sit there revising for hours and hours, you will get slow, tired and sluggish, and your brain is not going to get the food and oxygen it needs to help you revise. Take a break, get up from the desk and go for a walk. Clear your brain and then come back and start revising again. You will be more productive and get more done.

5.  Don't waste time
Don’t waste time making your revision notes look pretty.  No one else is going to see them. Your notes should be functional and clear. They should be concise. They don’t have to be pretty and all coloured in with tons of sticky notes on the margin. Use the time you have to revise smartly. Revision is about revisiting material to refresh your memory of material you have already learnt. It is not about colouring in! 

6.  Find your best place to work
Find the best possible place you can for your revision. Ideally, it should be somewhere comfortable (but not so comfortable that you fall asleep), somewhere quiet or noisy (depending on your taste) and where you have control over noise levels. It should be somewhere free from distractions (smartphones, Twitter, Facebook, TV etc.). Once you have found your ideal place, use it!

7.  The Revision Timetable
Make a revision timetable and try to stick to it. Work out how long you have to the exams and how long you have to revise each topic. Don’t fall into two of the classic revision timetable traps: 1. You spend so much time making your revision timetable that there is no time left to revise (see Rimmer in Red Dwarf for an example of that); 2. You spend all your time revising for the first exam and forget that there are two other exams a week later. 

8.  Don't just sit there - get some exercise
Studies have shown that going to the gym after studying can help you recall the material. Don’t spend all your time revising; get some exercise and get your blood flowing around your body.

9.  Don't just read, learn...
Just reading your lecture or class notes is not learning the material. You need to be active to strengthen your memories and understanding of your notes. The easiest way to do this is to move the information in and out of your brain. Read the notes, re-write them in a different style (or draw them as a mind-map or diagram) without looking at your original notes, and then check your new notes against the old. By doing this, you have moved the information into your brain (reading), out of your brain (making the new notes), and then back in and out of your brain as you correct your new notes against the originals. This approach to learning is backed up by several studies and has been shown to work.

10.  Mix it up a bit...
Just sitting there reading the same thing repeatedly or ploughing through your notes class after class is not learning; you need to alternate your activities to keep your mind fresh and keep learning. Try breaking your study up into small chunks of learning followed by a small test to see if you have learnt and understood the material. Doing this will keep you fresh and alert and speed up the learning process. You never know; it may even make it fun! 

11.  Test yourself
When you are revising, just reading the material will not make it stick in your brain so that you can magically recall it during the exam. You need to understand the material and make connections. You need to summarise and process the material. Reading is passive; learning is active. Try reading the material, and then after a short break, try recalling the material and checking your recall against your original notes. Doing this will test you, so you will know how much you really understand, and it will help you strengthen the memory of that material.

12.  Don't Panic!
During the run-up to an exam, it is very easy to dwell on little things that would normally be insignificant in your daily life and to start panicking. Don’t!  Don’t listen to rumours, don’t dwell on the trivial, and if there is a problem, speak to someone, a classmate, a teacher, a lecturer, or a parent. The key thing is not to panic and to keep hitting the revision.

13.  Tick! Done!
Hopefully, you have prepared a revision timetable, and you are following it. If you are, then one handy tip is to mark off your revision as you do it, as this will give you a sense of achievement and progress. It is always nice to tick something off on a to-do list.

14.  Treat yourself...
Constantly revising is not going to work. You will get tired and inefficient. You need to break it up. The easiest way to do this is by giving yourself planned treats. For each revised lecture or class, you could give yourself some time on Twitter or Facebook or watch some TV. Maybe chocolate is your thing? If so, then for each 30 minute period of study, you get two squares of chocolate or a biscuit (be careful, though, as this revision technique can lead to obesity). A slightly healthier option may be for every 30 minutes of revision, you go for a short walk. The choice is yours - treat yourself for all your hard work!

16.  Keep your brain active... Mix it up
Try to keep your brain active by varying the material you revise. Try something really tough, and then switch to something easy. Mixing it up can help you retain information and improve your understanding.

17. Stop looking at social media!
Avoid temptation. Try to get quality non-fragmented revision time. Stay off social media. If you are a social media junky, then use it as a treat to help you revise - for every 60 minutes of revision, you earn 5 minutes on Facebook or Twitter. Put the phone down, lock it in a drawer, and resist the urge. 

Saturday 4 October 2014

Looking for an ELISA plate reader, and why you shouldn't get a HumaReader HS

Before I start this post I would just like to state that the views expressed below are my own and not that of my employer.

For the last 18 months I've been trying to buy an ELISA plate reader, with no success.

Admittedly enzyme-linked immunosorbent assays (ELISA) are not new and have in fact been around for at least 30 years (I first heard about them during my first degree, and they were viewed as a replacement for the radio-immuno assay (RIA)). So, on the one hand you could be argued that the technology is old and well-established, or that it's a technology that is had its day. Either way you would expect the market to be mature and able to provide suitable equipment.

When I started looking for an ELISA plate reader I was struck by how old all the machines appeared to be (in a number of cases designed in the 1990s, and a few machines in the early to mid-2000s), the poor design of their user interface and how difficult it seemed to be to get data in and out of the machine (one company offered me a machine with an attached dot-matrix printer - I had no idea such printers were still made, can you even get the paper). What was really surprisingly was how few of the machines could be networked, and how old the input/output ports were on the machines.

What I was looking for was a modern machine that could easily export results either directly to a server, or to a USB data stick. You wouldn't think it would be that difficult to find such a machine? How wrong I was....

After two rounds of procurement (nothing suitable in the first round, so I dropped my requirements) I finally settled on the HumaReader HS as it appeared to be the best of a bad bunch. The machine, from what I could see in the literature, did have a rather clunky user interface but, and this was in my opinion it's big selling point, it did have two USB ports, a LAN port, and an SD card reader. From what I could gather from various promotional leaflets and the user manual, the machine was able to export data and methods to the USB ports, and it could be connected to a computer for direct export to Excel (see below). To me this seemed to be a good match as it meant we could easily collect and export data from 25 to 30 ELISA plates in an undergraduate practical and then redistribute the data to the students for analysis.

IMG 1276

The HumaReader HS ELISA plate reader - it can read plates, but you can't get the data out of it...

The machine was delivered to us after 8 to 10 weeks and installed. It was only at this point it became apparent that the export to the USB stick was in a proprietary format (Why didn't the engineers think to do a simple CSV export? I guess they were not very good engineers?) that could only be read by another HumaReader HS machine. I really cannot see a reason for wanting to do this? Maybe the methods when setting up a number of machines, but why the data?

IMG 1278

Ports on the back of the HumaReader HS ELISA plate reader - there may be data ports, but don't make the mistake I did and actually think you can export data

So, strike one, no USB export. So to my fallback plane... Export to Excel.

Unfortunately the HumaReader HS doesn't even seem to be able to export to Excel. When I raised this with the company (both the local supplier and the actual maker of the machine) I didn't receive a satisfactory response. In fact today I received the email below:

"Good day to you.
After several attempts, we managed to sort the data to excel format by using a customized Microsoft word Macros’ script.
The process is involved few steps as following:
1) Transfer the readings from ELISA reader to Laptop (LIS format).
2) Open the data which in LIS format to notepad, copy and paste the data to Microsoft word.
3) Sort the data by using a customized macros’ script and the data will be saved in excel format.
4) Open the excel format data and sort the data accordingly.
In Upon the sorting, the data is as following and for detail please refer to attach file."

Is the company serious? It would appear they are! To have to do this for 25 to 30 plates in an undergraduate practical would be an absolute nightmare. What century are we living in?


An extract from the HumaReader HS Reader promotional material...

How do other people cope? How do they get data out of the machine? Why would you design a machine from which you cannot export the data? Absolute madness.

Today I have told the company they can collect the HumaReader HS Reader from the lab, and refund the money.

So, I'm back in the market for an ELISA plate reader. As for the ELISA practical running in a few weeks? Guess I will have to be creative...

Declared conflict of interest: I am really interested and supportive of open data standards that allow the sharing of data between scientists and different labs. I heave worked on data standards in proteomics and was involved in establishing the 'Minimum information about a proteomics experiment (MIAPE) standard.

Sunday 10 August 2014

Is your teaching website mobile friendly?

Here is an interesting question... Have you tested your teaching website on a smartphone? If not, try it... I'll wait.

Many websites were produced before smartphones were really around (~2007), so they are not mobile-friendly. Your site may look great on a desktop machine...

But on a smartphone, which the majority of students now have, it may look awful.

It may look OK, but it is impossible to read, and almost impossible to use. In fact, the only way it can be used is by zooming in, which is fiddly and means that it is difficult to find your way around the site. Basically, students will get bored and not engage with the site, no matter how wonderful it is.

However, the site would look much better, and be more user-friendly, if is displayed correctly, and didn't require any zooming.

The solution to this problem is to rewrite the site so that it displays correctly (or is at least usable) on mobile and desktop devices, and this can be done using one of two methods:
  1. Responsive web design (RWD)
  2. Mobile redirect
Both these methods have their pros and cons, and I have used both approaches.

1. Responsive web design (RWD)

This, in my opinion, is the correct way to do things... However, there are some disadvantages to this approach.

A well-designed website should separate the content (the words and pictures) from the layout, and typically the layout of the page is controlled by 'code' in a file, that is separate from the content file, called a cascading style sheets (CSS) file, which is loaded by the 'content' page in the web browser. These CSS files control the way the page looks, that is, the size of the text, the fonts, the positioning of text and images etc., and they can control more that one page.

Designing a website that has content and layout style separated in this way means that if you suddenly decide that you want all your text displayed in white on a black background, instead of black on a white background, then if you have designed the site correctly you only have to change one file, the CSS file, and all pages on the site (and you may have one page, or you may have many 1000s) will display the text in that way. If a CSS wasn't used then changes would have to be made to each individual page, and for very large sites this could be a very time-consuming job.

This separation of content from layout means that if it is possible to determine the screen size of a device, i.e. it is a large desktop computer screen or a small handheld device, then different CSS files can be called so that the webpage is optimised for the device. And this is what happens, as the webpage loads the browser can run a test for device screen size and determines how to format the page.

The 'pro' of this approach is the content is displayed correctly for the device being used, and images and movies are shrunk to fit in the smaller screen. However, the 'con' is that even though the image or movie appear smaller their files are not reduced in size so pages may load slowly on mobile devices with low bandwidth.

I used this approach with my main website:

The browser detects the screen size and uses one CSS file for large (desktop and tablet) screens and a different CSS file for small screens.

2. Mobile redirect

With a mobile redirect, the browser still determines the screen size of a device, but in this case, if it detects a small screen it will redirect the page request to a webpage specifically written for mobile viewing.

The major disadvantage of this approach is that you have to maintain two sources of the information (text), that is, one source for the desktop, and one for the mobile. However, this problem can be resolved by holding the text in one file and loading this dynamically into the 'desktop' or 'mobile' webpages by using PHP or javascript. (As you can imagine this makes things even more complicated.) Another problem is the page may not be correctly crawled (indexed) by the search engines as they may not be directed to the mobile version of the material, and so no one may find it!

A significant advantage of this approach is that images and movies can be resized to better fit mobile devices and this means images and movies will be in smaller files, which will, therefore, load faster on mobile devices with low bandwidth. Again, this means that two versions of the image or movie file will have to be produced - one for the desktop, and one for the mobile.

Which is best for me?

This is a tough question. Both approaches have their pros and cons. Personally, I prefer solution 1, Responsive web design (RWD), however, for sites rich in images and movies solution 2, Mobile redirect, maybe a far better solution as pages will load faster and students will get a better experience.

Wednesday 11 June 2014

Say hello to the hairy tree rat.... The latest genetics model organism!

In a recent post - Designing a virtual fruit fly lab using HTML5 - I wrote about how I had replaced a fruit fly genetics 'wet' teaching lab session with an online session written using HTML5. However, one thing I didn't mention was that we invented a new 'model organism' for the assessment - The Hairy Tree Rat.

The reason we came up with the Hairy Tree Rat was that it had become apparent from the original practical that the assessment on fruit fly genetics was 'compromised' as all the answers were available online, which meant that students could 'google' a mark of 100%.

As it now says in the practical:

"You have been tasked with learning about a newly discovered mammal; the hairy tree rat. Found on a single island it seems to bear resemblance to the naked mole-rat but lives mostly in tree canopies and is hairy! The coat colouration is unusual; most of the rats are rusty coloured (like the tree bark) but some are brown and others are tan coloured. You need to work out the genetic relationships for colour; assume all rats are from true-breeding lines (unless the litter is specified)."

By doing this it means we can control the genetics, and we can change the parameters of the assessment, so we can now assess the students against the learning outcomes, and be fairly confident that the students haven't 'googled' the answers.

Sunday 1 June 2014

Designing a virtual fruit fly lab using HTML5

A few years back (20111 to be precise) we were faced with a 'crisis' in the delivery of a first-year fruit fly genetics lab. The students didn't seem to be getting as much from the lab as we would have hoped, and it was getting increasingly expensive and difficult to run the session with large groups (we had ~350 students in the year and we run the lab four times).

When the lab was first put together it was being offered to students studying the genetics degree. For them, it made a lot of sense as fruit fly genetics was at the core of the degree. However, when we introduced the practical to students studying other degrees in the school the session became problematic. Yes, it was needed as we felt that the students studying the life sciences needed the basic genetics training, but we felt the students were not really taking as much from the session as we would have liked.

Having thought long and hard about the problem we decided to make the lab virtual.

The problem

Having run a number of virtual labs over the years in bioinformatics and protein analysis I was aware of the problems involved in delivering such material and also how the static nature of a web page, and of websites in general, can be very boring and tedious for students. Click, click, click....

Therefore, it was decided that what we needed to do for the online fruit fly practical was to deliver something that was interactive and moved, and where possible reproduced some of the experiences the students gained in the traditional fruit fly practical. It was clear that there was a need for animation, and possibly some 'gamification'* (a word I don't like) to engage the students. It turned out that the solution to this was to use HTML5.

The solution

HTML5 is a new web standard for the language that describes how a webpage should look and feel in a web browser. HTML5 is not a finished standard (and judging by the speed that W3C is moving at it never will be a finished standard), and therefore it is in a state of flux and is liable to change. However, a number of the major web browsers such as Internet Explorer, Firefox, Safari and Chrome have already decided to adopt parts of the new HTML5 standard, and one part of the new standard that has been adopted, and was most useful for dealing with this lab, was animation.

Using the animation commands and tools that are available as part of HTML5 it was possible to produce a number of 'virtual' fly labs, and the final version of the practical had three such labs:
  1. Sexing fruit flies;
  2. Identifying fruit fly mutant;
  3. Determining the genetics behind the mutation.
All three 'labs' had the same underlying idea in that there was a small window with a number of fruit flies running around which the students were able to 'anaesthetise', so they stopped moving, and which they could then examine by clicking to get an enlarged image (see figure below). The students then answered questions associated with that particular section of the lab, such as what was the sex of the fruit fly, the type of mutation (if any), and determining the inheritance patterns for different crosses of fruit fly mutants.

Screen Shot 2012 02 23 at 07 24 02
Virtually sexing fruit flies

The above image is of the fruit fly 'sexing' lab - unfortunately I cannot show you the animated version of the lab as I am unable to add the necessary javascript to this page to get the flies to move.

Screen Shot 2012 02 23 at 07 22 46'Anaesthetised' flies

In the above image, the student has 'anaesthetised' the flies so they are no longer moving, and then clicked on a fly to get an enlarged view. The student can then answer the question as to the sex of the fly.

Two final problems - one mine, one HTML5

Coding up the lab was fairly straight forward and after some initial fiddling and debugging of the code everything was working. However, there were still two problems.

The first problem was that the virtual labs would only work in 2011 on the latest versions of the browsers for Internet Explorer, Safari and Chrome, and would not work at all in Firefox. For me, this was a real shock as I was expecting any problems to be associated with Internet Explorer. (It turned out that the reason the lab would not work in Firefox was that Firefox had not yet implemented one of the key animation calls that are used to control the animation.)

The other problem was purely down to my code, and I have still not got to the bottom of it. The virtually labs rely on a number of 'random' number generators and some trigonometry functions to control the movement of the flies. Somewhere in the code, I have something wrong because if I leave a lab running for an extended period of time all the flies end up wandering around the bottom right-hand corner of the screen. Although this does not detract from the experience of the lab, it is annoying!

Why do my flies end up in the bottom right-hand corner?


The lab was designed to run in a 3-hour slot with the students exploring the virtual fly labs for the first two hours, as well as completing a number of other tasks, including answering a number of formative questions, with the last hour used to start the online summative assessment. I was surprised to find that the students managed to work through the lab section in about 90 minutes, however, those that rushed the lab did find the summative assessment more difficult. I have now run the lab with over 1000 students in the past 3 years and this is a reoccurring theme, even when they are warned not to rush.

The lab seemed to work very well and there were no obvious problems or complaints on the day. The final marks for the online summative assessment were in line with other modules, and other work completed by the students, so overall I think the lab was a success and met the learning outcomes for the session. In the feedback, I have had from students taking the labs I have had no complaints.

One problem that I have encountered is the site does require significant maintenance as the code base needs changing every year as the HTML5 standard, and the support offered by the different browsers continues to evolve.

(* gamification is the use of game-like ideas and strategies to help students learn, that is, the students learn whilst they are having fun and playing a game. A sort of learning by stealth.)