Friday, 31 January 2014

This week in ColChambers: 31st Jan

Time for a look back at what happened this week on this blog.

New Articles

Thursday, 30 January 2014

Wimbledon: The All England Club - Court 1 as a 3d Model you can download

Another 3D model you can download as part of Google Earth is court one at Wimbledon.

The All England Club - Court 1

So excited to have models like this and Rod Laver arena. Using them will be fun.

Wednesday, 29 January 2014

Is Vanilla JS ready yet?

There are so many javascript libraries that I can't be bothered to learn a new one without good reason.

This tweet
♇4n3 ‏@Pl4n3 TIL vanilla.js mind=blown. :)
led down an interesting path. I visited hoping for some kind of demo. Nothing there. Then this line caught my eye

Vanilla JS is so popular that browsers have been automatically loading it for over a decade.
hmm.  Now that is interesting. Checking back to the tweet p4n3 is a 3d guru I have respect for. If he is using it I might be interested. Looking through the speed comparison tables was worthwhile.

I was hoping that javascript itself has matured to the point that the need for libraries is reduced or non existent. Thankfully that is what this site and the tweet is about. Worrying less about what library you use and more about solving problems that matter.

The link to Vanilla JS documentation points simply to the Mozilla Javascript page.

A few reviews make interesting reading when comparing native js with libraries

Each highlights that native js can now replace the need for several aspects of libraries. This is good news. I'll keep an eye out for places I can use it

For me though I'm going to wait. Simply because it's an evolving area. A few more years and I might just be able to write pure JS. Right now though I have to figure out which works every where and which doesn't in some random case. I have a life too so I'll let others tell me when it's all ready. 

Glad to hear JS is well into its journey to maturation though. 

Tuesday, 28 January 2014

Pairing vs. Code Review: Comparing Developer Cultures

Inspired by a great post Pairing vs. Code Review: Comparing Developer Cultures  by Paul Hinze of So Create I wanted to keep this for reference. We do code review in the VLE team at the OU but not pair programming. I can see its value but I am much more in favour of variety of approaches then only using one. You might favour one over the other but in most instances it's more important to have a few options and you git the approach to the solution.

That said I've never done pair programming. I'd like to try it just to see what it's like but I expect to get nervous having someone stare over my shoulder like a back seat driver. I've done something close like I think we all have. That is ask some one for advice and we then try and solve the problem together. You start writing code and essentially programme as a pair. The difference is that you are still the sole responsible person for the task. It didn't start out as a joint task.

So reading some one elses experience seems useful. One particular aspect I'm looking at is the economics involved. My degree included management and it gave me a passion to understand the long term value of things. Pair programming seems great for quality but you're paying two people to complete a task. So it's a bigger investment than paying one. Is the return worth it? That's a very open question that's more about interpretation and personal choice than fact.

Here I summarise what I have taken away from Pauls account so I have a good record to refer to quickly.

Prerequisites for success

There are a few nonnegotiables that are common across both of these paradigms.
  • Solid continuous integration - builds that run on every commit
  • Talented core developers - these folks helps promote quality and drive the architecture of the codebase
  • Agreement on the importance of code quality - the team and the overall company both recognize the value of maintaining a high-quality codebase
  • Iterative self-organization - the team is willing to collectively evaluate their process and course-correct on a regular basis

In my experience these things are all necessary no matter what process you decide to use.

Advantages of pairing:

some of the advantages Paul has found with pair programming
  • high bandwidth communication between pairs
  • You can train junior developers easily by giving them an experienced pair. 
  • Core developers can spread best practices and knowledge silos across the team quickly. 
  • New tools and techniques are shared naturally across the team. 
  • Everybody gets better together.

Dis Advantages of pairing:

The disadvantages paul has found are:
  • Pairing is sensitive to team balance: Pairing experienced people with junior and over stretch the experienced staff, It can also break down knowledge silos but also make it hard to find good pairs. One knows the area well, the other doesn't and slows the team down.
  • Pairing culture can breed monoculture
    • can make it tough to hire people. Not everyone likes constant pairing and working closely with the same person all the time. It can be harder to introduce different tools and approaches.
  • Pairing does not lend itself to problems requiring in depth thought like system design and architecture: Particularly an experienced programmer paired with a junior. Teaching while solving a difficult problem is a particularly tough challenge.
  • Sometimes you end up needing code review anyways

Advantages of code review

Paul feared the transition to code review but actually enjoyed the experience. Some benefits were:
  • the positive motivating pressure to perform well is still there.
  • In contrast to pairing, there are no barriers to taking on deep thought problems.
  • lends itself to a wider pool of personality types that can be effective
  • Code reviews are asynchronous
  • forces you to think about your values more

Dis Advantages of code review

  • being alone: less camraderie
  • more emphasis on your own self control. You can be lazy.
  • reviews and associated discussion can stack up
  • conversation happens after something is built. 

What's best?

My view is that they are both useful. What's best depends on the problem at hand and environment. Paul agrees. He finds both work well. His closing note emphasises the focus on quality not workflow.
So if you don’t have one already, find a team that cares about code and about process and you can try to solve some of these problems together.

Monday, 27 January 2014

Blogging Platforms: A look at Wordpress

In my search for the right blogging platform for me I expect to go with wordpress unless a recent alternative shows up. This is a post I am writing as I go. I'm hoping to make a decision in the next month or two but life often gets in the way and deadlines drift. That's life. I keep notes like this all the time but it's the first time I've made them public. I have just noticed how much I benefit from others sharing their notes so I am doing the same.

So the obvious questions are
  • what I actually want to do with blogging?
  • why wordpress? 
  • what does WP offer and why is it better than blogger. 

what I actually want to do with blogging?

The first question is what are my needs for the future?
  1. create content: It's relatively easy to create content right now but I feel it should be much easier. The blogger mobile app for example ruins the formatting of existing posts so I'm put off using it and rely on desktop browsing. Not good. Lots of other issues.
  2. connect: Blogger connects easily to google plus but nothing else. I'm looking at other options like livefyre. I want automatic publishing to major platforms. Though IFTTT and others get around this.
  3. promotion: It's a lot of work right now to promote what I do. I hear wordpress has a lot of plugins to help
  4. monetise: Blogger does well so far in allowing adsense but overall the feeling is amateurish and the stats seem unreliable
  5. Admin: Blogger doesn't have great admin tools. The mobile app doesn't even report stats.

Why Wordpress? 

Wordpress is the tool for the majority of bloggers I know of or hear about, professional or amateur. My experience of wordpress has really impressed me considering my 7 or see years experience of blogger

Quick Review

My wordpress blog life as play gives me a basic insight into Wordpress. I started it a few years ago but left quickly because there were a few things I couldn't do. Mainly it was about restrcitions on what you can embed but now I don't have the same concerns. If I host I should get round any problems anyway.

So I thought I would just list the features I really like:

  • The editor: 
    • putting it fullscreen is lovely 
    • pasting test in is easy. Blogger needs a lot of formatting
  • Quick draft: Now I have found it I love it. Something I've been needing
  • php and opensource: I'm a developer who write php code all day. So the ability to adjust wordpress if I need to is a nice option to have. Not expecting to do anything but this is not an option with blogger. 
  • related posts: Categories done as I have always expected. Every post ends with a list of related posts determined by the categories it is assigned to. With blogger I'm having to do this manually. What's the point of that?
  • Social: 
    • Blogger does an OK job. Publishing to G+ was particularly good until I started scheduling posts. Now they don't appear there unless I share manually. What's the point.
    • on tennisfrontier I can post to all the big networks but also customise the post to the network. Set key tags for each using @, # or whatever.
I also post on tennisfrontier which runs wordpress. This is properly setup i.e. not the basic hosted package so I get a chance to see more of the plugins that are available. The content sharing and promotion options are much better. Particularly the ability to coordinating social media campaigns for each post.

I am still learning what wordpress can do by running my blog life as play. It's the next blog I want to focus on and now I'm a starting to think properly about it.


I am likely looking for a hosted service. Thought I checked with a frind who set up a self install wordpress site. He said wordpress isn't particularly secure by default. So most of the work was in setting up the right security plugins. He chose these:
  • BulletProof Security
  • Look-See Security Scanner
  • WP-Sentinel

Self hosted

So I just found some guides for transitioning from blogger and wordpress to self hosted word press. I know there will be a lot of these out there and planned to search in time but I came across these today. Worth including


Word press is all about the plugins so I looked at what is popular then checked a few more sites:

Tutorial sites


I use git a lot now. I basically swear by it. I'd rather use this instead of ftp if I could. So, naturally, I'm going to look at how to use it with my hosting and with word press.

Sunday, 26 January 2014

Australian Open: Rod Laver Arena as a 3d Model you can download

Of course I love looking for 3D models that I can use. Preferablyl stuff I can use straight away in Unity but you can normally convert them if needed for Unity. The process of importing seems to be a skill in itself anyway.

That aside I'm listening to the Aus Open 2014 and realised I had never seen Melbourne Park where it is played. So with the wonders of modern technology I can do the next best thing. A 3d tour of sorts.

So I jumped into google earth and searched for Rod Laver Arena and Voila. I love seeing how these tournaments are laid out. It's always different to how I imagined but now I know it adds a little to the experience.

Imagine my excitement when I found that Rod Laver Arena has been modelled and you can download it (apparently for free)!!! I know. I was floored too. Properly salivating.

I can't see a way to embed the visualisation here so a link will have to do.

check out Rod Laver Arena 3D model

Watch this space for the upcoming models I am so excited to list :-)

Building my portfolio of models I can use in Unity is an on going quest. I already have a whole gamut of Nasa models. No joke Jupiter orbiters and apollo rockets no doubt and the amazing space shuttle. No joke. Downloaded from Nasa itself. I'll post the link in due course but if you want it just get in touch.

Thanks for dropping by. I haven't used this Rod Laver 3d model yet so if you do please let me know how it turns out. If you need to do some jiggery and pokery :-) to get it right, which I find you have to do with all models, then it would be great if you share what that was.


Saturday, 25 January 2014

Git: Fixing “Your local changes to the following files would be overwritten by checkout”

Git is quite a learning curve. I get the feeling I can now call myself experienced because I'm starting to search for quite indepth solutions.

Today was how to get past the error message “Your local changes to the following files would be overwritten by checkout” when trying to switch branch.

The fix was actually straight forward in this case.
git checkout filename
 The background was more interesting.

  • git status showed no differences
  • gitk also showed no changes
  • this is because I am using git --assume-unchanged a lot more for key reasons
It's the --assume-unchanged aspect that complicates things. I'm not happy to have to do it but given the work I have to do and the rules that go with it it seems the best option. That is a discussion for another time. For now this answer helped me so I hope it helps you. 

I'll now go into a little detail why the fix wasn't as obvious as it seems by showing the symptoms you get when you use --assume-unchanged

The extra detail I got from the error message was 
Please, commit your changes or stash them before you can switch branches.
It is this wording that introduced the complexity. Git was telling me a file was different when I called checkout but not when I called status ot gitk. Confusing 

My search didn't give an answer straight away. Had to do a little hunting and of course the answer was nice and simple. 

I tried:
  • git stash:  no joy because no differences were found on the branch
  • git stash save --keep-index same as git stash. No difference to stash.

Friday, 24 January 2014

What is snappytv?

During the Australian Open I saw a replay of tv coverage on twitter. Shared only a few minutes after broadcast on tv. I couldn't believe it.

The tech used was snappytv so I had a quick check.

How is it done, How does it work

Where to use it

That's the key question. I assume you need to be streaming live tv. I haven't used this yet to I don't know if it works on all streams etc. I'm now thinking of uses mainly because I feel there are things I want to do that this will facilitate. 

What springs to mind is player characteristics during matches. Where they stand to return or rally and position at net. That kind of stuff. 

The shortness of the posts attracts me because I like tools that help you get to the core of the matter. 


Of course this means I need to learn a little about the rights issues involved in this type of work. 


An exciting idea. The first use I have seen of it really impressed me. :Lets see if I start using it though. 

Thursday, 23 January 2014

Blogging and comments: Livefyre Wordpress only?

Part of considering the best blogging platform for me and investigating word press is considering what I lose migrating from Blogger. Blogger has been  particularly slow recently thus taking more time to work with. That's annoying but a topic for later.

Right now I'm considering comments. Blogger gives you something because it's built straight in to google plus which is a growing platform that's increasingly useful for traffic and discussion but it's only one place. I'd rather connect to all and let my visitors decide how they want to connect.

I've seen livefyre on several sites and found it useful. so I checked it out a little more.

Default Install

Is it a no brainer or a bit of work? You get 4 options as standard

  • wordpress
  • tumblr
  • custom
  • Joomla
Implying wordpress is a no brainer install. 

Blogger install

Can you add livefyre to blogger then? a quick search apparently you can

Doesn't seem too hard. Next question is which of my blogs I might try it on.

Wednesday, 22 January 2014

Gene Experiment

Here is another approach to exploring horizontal gene transfer

If you have created some simple bacteria in a virtual world like Unity3d. They don't have to be complex, just cells or even just spheres. Get them to move around a petri dish. They could have a nucleus and inside that they have genes as scripts. Each script has an effect like:

  • glow in the dark
  • turn red, green or blue
  • get longer or shorter.

You can then selectively knock out these genes and see the effects over time on them and their offspring. You can mate the bacteria to see which genes are expressed. Just an experiment on genetics. Something to share and start the ball rolling. Save everything in json so anyone can use it.

I expect this has already been done elsewhere. If so great but most examples aren't designed for others to build on. That's the idea here.

  • Unity is free to use
  • the code required is relatively simple
  • sharing the application and source code with others is relatively easy. 

Not only do you demonstrate the principles of genetics and gene transfer but you teach others that they can practice the principles of biology directly through digital research.

That is what really excites me about knowing how to program. I don't have to wait for my cell culture to grow. The only limit to what I can learn is my imagination. I can literally create my own laboratory and experiments whenever I wish. Fun :-)

Tuesday, 21 January 2014

Frozen is nominated for multiple Oscars

Yay. Very excited to hear that Frozen was nominated for a bunch of oscars including
  • IDINA MENZEL: Singer, Best Original Song, “Let It Go”
  • JENNIFER LEE & CHRIS BUCK: Co-Directors, Best Animated Feature, Frozen 
  • BOBBY LOPEZ & KRISTEN ANDERSON-LOPEZ: Composers, Best Original Song, “Let It Go”
I didn't realise it was getting quite that kind of attention but it's really nice to see. I love the film and so did our toddler so it's nice to hear it getting the success I think it deserves.

The Plague and the benefits of Horizontal Gene Transfer

How do you express the concept of Horizontal Gene Transfer in a way most people could understand and also see where it could be useful?

In fact I have several related concepts and questions I think I can express in one idea:

These are the challengea I've been considering for a few years. One idea I like is creating an experiment to demonstrate the concept in a historical context. Once I understood Horizontal Gene Transfer I quickly started to wonder if this would be a simple answer to why certain people are immune to pandemics like the plague while others aren't.

The point is that anything that would help you survive the plague would be selected for in an evolutionary fashion. Even in the most deadly plagues and pandemics there always people who are immune and survive. It makes a lot of sense that if this immunity were the result of a viral infection then it could spread.

As long as the virus doesn't harm the individual enough that they don't survive then the virus would actually help people live when those around them would die. This would become a symbiotic relationship as long as the plague lasts. It would also encourage the transmission of the virus. Those who are immune would obviously become more common relative to those who are not immune. Stories of miraculous recoveries by being touched or in the presence of certain immune individuals would be abound.

Viruses survive because they can change the genetic code of the hosts they infect

This may sound fantastical but the concept is already in place and called active immunity. The individual themselves would produce the immunity. A related example is Sickle cell anaemia. It is dangerous and uncommon in normal populations but more common in places where malaria is prevent.

Sickle Cell Anaemia protects against malaria. So while normally it would be a bad condition to have but in an environment where Malaria is common is would be quite a benefit. So it demonstrates the principle of an affliction being an advantage however Sickle Cell is an inherited genetic disease.

All we are really talking about here is for nature to come up with a way of being able to transfer this condition to others. That's actually what viruses do. In fact it's how they live. Viruses survive because they can change the genetic code of the hosts they infect. Otherwise they wouldn't be viruses.

So that's the basic theory. A virus uses horizontal gene transfer and could infact do good instead of harm. Giving a species selective advantage. How to demonstrate this though, that's a fun challenge.

We have always known more about evolution and biology than we think. We just haven't appreciated enough different viewpoints. 

So the context is the plague. I'm obviously thinking of the great plague that affected Europe in the middle ages and came to England because I'm English. You pick your own similar story that interests you. The concept is most important.

Working in software is for me an advantage. I practice horizontal gene transfer on a daily basis so the concept and its application becomes quite straightforward once I'm in the right mindset.

The story I want to follow is of a cell or cells being attacked by plague bacteria. You must introduce a virus containing code to protect against the bacteria. Essentially an update to the cell code base. Now the exploit on the code has been fixed.

This explains in one example how a virus could protect us against infection and thus be beneficial. Not just harmful. And how our genetic code can be constantly updated through exposure to the world around us. Just like our devices and apps are constantly being updated.

I described how to translate this into software so this article is about putting context and story behind the techniques. Why you would bother to create this app and why Unity interests me so much as a development platform. You could do this through html 5 but I think it would be easier and have more impact through Unity.

Overall This demonstrates neatly my view that we have always known more about evolution and biology than we think. We just haven't appreciated enough different viewpoints.

Monday, 20 January 2014

Where to buy domain names?

A question many of us have is where is best to buy a domain name from? and also should I try a new supplier? That's what I asked when I wanted to buy a domain name. Here is my journey.

I've been using 123-reg for almost a decade now for some basic reasons. Mainly because they fit the bill at the time. That was

  • They don't lock your domain in. You can move it to another host at any time. I heard of companies acting as though they own your domain and expect a release fee for it or won't even let it go.
  • Good prices: One of the cheapest at the time
  • Redirecting: I just point my domain at this blog. No extra cost.
  • Easy renewal
  • Simple tool to find the best domain name at the right price. checks for all major domains e.g. .com,, etc at once. Tells you what is available, price options etc
  • Ok admin panel: You can do all the basic things I might need to do. Change where your domain points. change DNS and nameservers, web forwarding
  • Ok support site: So far I have found the answers that I need
They were the best on this criteria years ago and seemed ok since. Yesterday though I tried buying another domain name and was frustrated with all the extras they kept trying to sell me. It felt like if I forgot to remove each one in each step then I would get overcharged. 

I hate that style of business but I thing this has always how 123-reg have done it and I just put up with it. I know I don't need the extras and I don't buy domain names often so I ignore it. 

I just felt it worth checking to see if there is any thing better out there. Just a quick check. I know 123 and they don't seem to have changed much but it's always nice to look around. 

New features: Do I need them

The reason I'm looking again is because I have forgotten whether I need the stuff 123-reg tried to sell me. Things like:
  • Mail accounts: My memory is that this is irrelevant to your domain. Tied to your hosting instead. Hosting isn't something I would get with 123-reg. 
  • Whois privacy: A new thing to me. I assume it's just ex directory for domain names. I dont want to hide my address at this point. Some people will. 
  • hosting: as for mail. I get it elsewhere


123-reg email forwarding

This quick check reminded me about email forward.
  • Tried to set it up email forwarding at 123-reg that worked fine
  • Forwards show on the manage email admin screen only when you choose the relevant domain
  • Tried the advice on adding a catch all forward it didn't work at first. Said "incorrect forward recipient". Not helpful and frustrating. Turns out I already had a catch all forward set up. didn't know because the manage email screen doesn't show yoru forward rules by default. Removed it then added the new one.


I stayed with 123-reg in the end. Mainly because I've not had any problems yet and the others I found weren't any better. I only had 20 minutes to compare but the key point is that with these guys I'm not locked in. So the price was right and the risk is minimal. The admin screens are very clunk but for now I am getting what I pay for.

After sales

This is often most important to me. So I thought I would share a little of what you get and why I'm not in a rush to change once I find a company that's ok. Domains are cheap but crucial. With the wrong supplier you could lose control or not renew or something. 

Don't worry about who I'm with. It's more about know what you should be getting. I don't know everything I should be getting because it's just one aspect of putting a web site and app or blog together. 

ICANN verification

I got this straight after my purchase. I haven't shared the whole mail. Just the important intro bit

Please be advised that as of the 1st January 2014 it has now become a mandatory requirement from the Internet Corporation for Assigned Name and Numbers (ICANN) that all ICANN accredited registrars verify the WHOIS contact information for all new domain registrations, domain transfers and registrant contact modifications.
You have received this email as you have recently registered one or more domains from 123Reg/Webfusion with the following registrant details:

  • Invoice: Obviously key.  Came through instantly with attached pdf. e

Direct Debit

Direct debit confirmation: I set up a DD and the email confirmation came through quickly with full details of supplier 123-REG, 5 Roundwood Avenue, Stockley Park, Uxbridge, Middlesex, UB11 1FF, UNITED KINGDOM,, 17 / Jan / 2014 the mail gave the correct details and support info was

If any of the above details are incorrect please call Customer Services as soon as possible on 0845 450 2310or email us at However, if your details are correct you need do nothing and your Direct Debit will be processed as normal. You have the right to cancel your Direct Debit at any time. A copy of the Direct Debit Guarantee is below.

For information, the collections will be made using this reference:

References for support were given so I should be able to contact customer support and have a correct reference number making the process much faster.

Sunday, 19 January 2014

Virtual Worlds in Unity: Gone Home: what happened to the Greenbriars?

Has anyone played this game? It sounds fantastic. I've been tracking Unity for a long time and developing with it has been a real pleasure. Finally I am seeing Unity hit the mainstream as both a game and simulation platform. This title particularly is something that I am considering buying.

The concept seems genre defining. I love crime dramas, this sounds like an interactive one. The synposis is

A multiple award-winning story-exploration game that asks: What do you do when you get home and your entire family has disappeared? Spend your time going through their rooms to find out what’s happened of course.

Gone Home
by The Fullbright Company
for Windows, Mac and Linux

I head about it from the monthly Unity news letter. The promo video seems amazing and about gone home on the makes site tells you more.  What interests me is the concept. The interactive aspect of solving a crime. Moving from the passive process of which TV or film to the more interactive nature of games.

Whether the game is good is less important than the value that the gaming experience can bring. The genre is very young compared to the big or small screen. So seeing it evolve and grow is what really excites me.

If you can tell me any more about it. What is good, what is bad. Is there anything new to the concept, gameplay, interactivity that moves the genre on?

Saturday, 18 January 2014

Build a Virtual Body: Bacteria communicate with their hosts

This article Communication between bacteria and their hosts is the kind of thing I look for to support my dream of a virtual body. My interpretation is essentially simple.

I consider bacteria and viruses to be to the human body like plugins are to software. The body is an entire organism but in fact it's a symbiosis of multiple organisms that evolved together. These organisms are so interlinked they couldn't exist separately.

Normal evolution means that the body must continually keep up with the changing environment in which it lives. Bacteria and Viruses are simply natural means to facilitate these changes. Horizontal gene transfer is part of this mechanism and there is plenty of evidence that the organisms we host talk to each other. This is just the same as software and operating systems. They all talk to each other. Lots of tiny applications and scripts slowly get incorporated into software and ultimately built into operating systems. 

I simply see the same pattern happening in biology. In fact I feel that we are just seeing the normal processes of evolution occurring in digital fields as we have seen in the biological ecosystems. 

Friday, 17 January 2014

How could you build a virtual human body?

My idea in a paragraph

I want a virtual body to facilitate research, teaching and general understanding of how we all work. The more we understand how we work the better prepared we are to maintain our bodies given the daily challenges we all face. I want to see a human body exercising, zoom in to see the heart pumping, zoom further to see the blood platelets rushing through, zoom further to see a blood cell. Then zoom inside to see the cell contents, then further, to the oxygen and carbon dioxide. So I could zoom in and out of cells, organs and even people to see what’s happening at every layer.

Here’s a bit more detail about the where, why, and how

Games already simulate human activities over time and I'd show how simple cellular mechanics have the big impact they do. You'd be able to zoom into the cell and see what happens, then zoom out again to see the wider implications. You can fast forward in time, go backwards, pause. And highlight cells or organs and change values. Because it's digital you can save state and share it.

Now we're getting to the creative aspect. A virtual laboratory. Your lecturer asks you to figure out why diabetes is occurring in a given population. You work on this tool that has the population and tweak their lifestyles looking for the answer. Reading the research you hear about glut4 a glucose transporter on the cell walls. They are activated by insulin and fit people have more of these than unfit. The transporters regulate carbohydrate flow from the blood to the cell. Hence you've found a reason why fitness could be directly related to diabetes risk. You experiment with the settings now you know what to look for. You set up your virtual experiment and get the results. You've now got your answer. You export your settings, send to a friend who confirms it. Then send to your professor and receive an A.

It surprises me that the means to build this exists yet it hasn’t yet been built. it's the definition of good science. Repeatable, sharable, uses standards etc. Year on year it could improve with more knowledge etc. so you could test more.

I'm probably not the first to think of it, but I don't see one on the market and I don't see any reason, why it can't be done. It's incredibly difficult but it's definitely possible. I might take the rest of my life and then some but it would be an amazing journey.
The best example I can find of an existing project is the Virtual Physiological Human program headed by Professor Denis Noble of Oxford. It is a very well funded programme that seems to be delivering at a fantastic rate.

The only problem with this is that it is a closed project delivering software and tools for health and medicine but not for everyday people. So I'm very happy to see the progress of the VPH project but I don't feel it will help me or the average person any time soon.

I have a lot of research in this area which I will add to this post in time. For now I just want to start the topic and provide a place to relevant details as I go. This is one of the most core articles to this blog. I've been investigating this topic for almost a decade now and is why I will often cover wider topics like technology, programming, marketing, economics and other areas in detail. They become important when you consider such a lofty aim.

Virtual Cell

Of course the first goal is to build a virtual cell. My plans have always been to build something incredibly simple. Share it and go from there. I've already built a very simple cell in using Unity as my 3d software. I've searched around and tried many solutions including html 5 but found unity to be the best for what I need.


Until now I've very much been wondering where the best conversation are happening. Current topics include

Related Topics

Useful Reading

I have found so much research I will post it here and then start to organise it as I go.

Useful Projects and Tools

  • centre of the cell
  • cell designer.exe
  • biomodels database curated set of models viewable online: BioModels Database is a repository of peer-reviewed, published, computational models. These mathematical models are primarily from the field of systems biology, but more generally are those of biological interest
  • cellML 
  • biopax (biological pathway exchange) a standard language for exchanging . BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups
  • Human protein atlas search for proteins or genes and find protein expression profuiles, subcellular localisation, transcript expression
  • david bolinsky presented the inner life of a cell on TED. They have a vision, along with harvard, to explore biology through immersive applications.
  • The gadget show : a recent programme simulator challenge part 1 part 2 showed simulations helped the team pass real life challenges like learning to fly and achieve a high grade in martial arts entirely through simulations. The first time ortis flew a real plane was during his test which he passed. The first time jason met a real opponent was in his grading which he passed. 
  • wikipathways: In the new tradition of Wikipedia, WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community
  • bigcat: turning heaps of data into biology. department of bio-informatics at Maastricht University
  • Simulation-based textbook for Cancer Biology The textbook utilizes a dynamic simulation approach and software, Cell Collective ( Mammalian Cell Cycle), that enables students to learn about biological systems from a systems and dynamical perspective rather than by memorizing static pictures of pathways in textbooks.
  • Andrew Hessel: Programming Living Things - The Next Generation Of Computing a fascinating talk explaining how synthetic biology allows us to build DNA scripts and update bacteria like you write computer code or put lego together. I think that tied to Unity a lot of fun could be had.

Personal informatics

How to track your life and get data to analyse

Existing informatics

Science libraries in javascript

Apis for each scientific discipline. What lots of us need are basic physical, chemical and biological processes coded as basic function calls of an api. Thigns like the krebs cycle and photosynthesis, foir biology the maillards reaction for chemistry, not sure what for physics. It really depends on what you want to achieve but long term wouldn't it be nice if the equations had already be converted to code and you could just implement the appropriate api.

Could be modelled on jQuery. We need libraries and apis that do standard calculations for each science. No sure if the jQuery approach fits Just create some basic examples first. 
jPhysics, jChemistry or jChem, jBiology

Thursday, 16 January 2014

Is there a good Blogging platform using Node.js?

So I'm considering a new blogging platform.

However I like to consider my options and see what else is out there. Node.js interests me because I am a programmer and Javascript was the first code I learnt professionally. I actually used JS with ASP, yep that's a pretty rare combination, to do a lot of server side programming. So Node.js is just the same concept to a much higher level and it's very popular. I understand it power twitter no less.

If you have any ideas or recommendations please comment or get in touch. I am always open to ideas.

So. My quick search for node js blogging platform returned

  • interesting. Sponsored by microsoft, is that a good or bad thing? seems slick, young and focused on simplicity. Is it too new, will it last. 
  • poet hmm a blog generator. What is that. Open source, maybe it sets up the infrastructure for a blog.
  • blogging module at nodejsmodules a list of popular blogging modules for node js for reference. Haven't reviewed it yet.  

Wednesday, 15 January 2014

What is the best blogging platform for me?

I'm looking for a new blogging platform. Blogger is great but it's the freebie and newbie platform. Not designed for serious needs but for beginners needs and getting people into the world of the web through writing.

I'm now really serious about my blog so I need serious tools and kit and thus the search begins. The obvious choice is Word press because it's pretty mature and used by everyone, particularly professional bloggers. if it's good enough for them then it's good enough for me.

I'm planning to buy some hosting and put a bunch of software on it. One will be my blogging software along with Moodle as a learning support tool (I use it at work at the Open University so it's a natural fit). So my questions are around what kind of hosting I will need. I also use and love cloud9ide for developing web apps in the cloud and the browser. It's the best I've found. I don't necessarily need something that hosts cloud9 software but hosting that allows publishing from github.

You can see it's a wish list to support a better workflow than I have now. If you have any ideas or recommendations please comment or get in touch. I am always open to ideas.

A look at wordpress
search for Wordpress Hosting
must have plugins for wordpress users

Related Articles

Tuesday, 14 January 2014

Good physics is good business

For every action there is an equal and opposite reaction, also known as the conservation of energy. These principles govern business just like they govern physics. The energy of a business can be money or the energy of staff or customers. The conservation of energy can relate to the need to be efficient. Using a small amount of energy to unlock huge amounts of energy is the goal. Just like in physics.

I just visited cost co and saw this in operation as a driving force behind a very streamlined business. Everything is focused on getting people and goods in and out very quickly. Turnover is high. Waiting is minimised space and profitability is key.

I keep seeing these principles in biology and business. This is just an observation I thought worth sharing. I wouldn't be the first to try and extrapolate from laws of physics to higher levels but it’s an idea I will be putting together over time.

Much of what we see in business has followed similar laws throughout the existence of human society. Cultures and tools have changed but the essence is about good relationships and taking advantage of opportunities. So the basic idea that one mans loss is another mans gain is the exact equivalent of every action being an equal and opposite reaction. If we look at things through this frame of reference and the physical laws really can help us understand the laws of business or any other system.

The troubles in the West represent opportunities for the East. We certainly see that reaction playing out. In the West the shift from boom to bust has hit the building and property business but encouraged the debt and recycling industries. It's not a judgement just the natural state of play.

Each era has its winners and losers which represent the equal and opposite reactions. Viewing events this way just makes business feel a little more predictable. As though, like with physics, if we know the history of an event and what generally followed the chances of similar events recurring are high.

However it is true that in physics we finally know so much of what we need to know to predict the likely outcome. At higher levels like business we cannot be so exact. Though that doesn't mean we can't see the overall patterns and act on them, if we know where to look.

Of course this analysis just poses more question that it answers. What kind of information and how much of it do we need? How do we know which pattern is being played out and which will occur in reaction?

Monday, 13 January 2014

Fit the learning style to the individual. How to use a semicolon - The Oatmeal

I am a big believer in fitting the message to the person you are trying to connect with. This very much informs my philosophy on teaching. So I like to use play as much as I can. Put a student in a place where they are playing with a subject or skill and they will push their boundaries without realising.

The learning is less conscious and more automatic. Done well, both student and teacher enjoy the experience with the teacher being a guide and facilitator. The experience isn't overtly about learning and feels quite natural.

So I came across this guide to the English language from one of my favourite comics The Oatmeal. It specifically focuses on punctuation and How to use a semicolon. It reminds me what good teaching. You can be pedantic, have real attention to detail and still make people laugh and learn.

This makes me want to learn about the semi colon and inspires me as a teacher. Reminds me just how much fun it can be to learn.

Thought you might like it. It's also a reason to ask the question. What have you learnt through play and entertainment? I can think of so much. How about you.

Sunday, 12 January 2014

Beginners zen

I just edited a previous post Zen Mind Beginners Mind and I also recently finished the book 'Mastery' by George Leonard which I really enjoyed it. Both have renewed my interest in the Zen approach to life.

So I had a little search for beginners zen. and found some really interesting articles
Just a simple post for those into zen like me.

Saturday, 11 January 2014

Updating cells through Horizontal Gene transfer: An idea for a game

My interest in biology runs so deep I enjoy coming up with my own theories. If you've read my blog you'll find many. Of course what is most exciting is when I find that a theory I have developed from my own experience and logic turns out to be real. The process of horizontal gene transfer is just that and is becoming more widely understood as a far greater force for evolution than sex.

 “The human genome includes sequences derived from viruses.”  Page 135 of The mathematics of life

Not only did an understanding of software development and thus code help me understand this most basic aspect of allowing a cell to upgrade its DNA but I feel it has great potential to express science concepts particularly biological ones.

That's the reason I have been exploring HTML 5 and 3D technologies including unity for the last few years.
From what I have learnt I think I can now show the concept of horizontal gene transfer in ways it hasn't been shown before.

The challenge I face is one of resources, time and money being a big issue and skills. I don't know the 3D virtual worlds arena well enough yet. So I thought I would simply describe the basic specification for the small game or app I would like to develop. If you would like to help in some way please let me know. I have so many of these ideas that aren't really that hard to put together but other constraints get in my way. It's the bain of our lives isn't it. Hopefully this is of use to some one.


The basic concept is that human code like PHP, Javascript, C etc already has many of the characteristics required to demonstrate Horizontal Code Transfer. If you consider the concept that many pieces of software like moodle, wordpress or web browsers allow plugins. The plugins work because they are designed for the target code base. They do what is necessary in the target code base to achieve their ends. That is pretty much how viruses work. They are targeted for a particular species and have a specific mechanism by which they adjust the target DNA code.


To keep things simple lets just focus on a cell, ignore the other cell components for now just have a nucelus and a virus. The virus contains the new code the nucleus. contains the target code base. The virus gets into the nucleus and delivers its code.  The concept is simply that the new code is a script/plugin written for the target code base.

In Unity3d this is actually quite a simple game to create. I've done most of the work already but the time to put it all together hasn't arrived. If you want to know more just ask. I want to be able to teach this to my son when he is older because it is such a fundamental way that our bodies work. Now that I understand it I can't tell you how useful it has become.

An experiment

I would create an experiment. Have a cell with a nucleus with a script attached that controls the nucleus and cell. A virus gets through. It has a script attached. It attaches it to the nucleus. The new script adjusts the existing configuration of the cell. Using the existing nucleus as a code base. It then creates more of itself.

It's an experiment to show It's possible in code and the mechanisms behind horizontal gene transfer. An added bonus is that a knowledge of software creation is can help understand it. I would then look at ways in which this could benefit a cell. Much like an update for your favourite program.

Modelling evolution

Using the cell model I was building. I would start to assemble the cell through evolution like this. I would then make a game around it. Maybe the player manoeuvre each element into place, or players build up their own cell and lots of viruses try to attach. The player has to get the useful viruses in place while avoiding the bad viruses .

This could be an open source game like a cell manager. You play the cell security. Choosing which viruses get through.

Friday, 10 January 2014

What works for nappy rash

This post is the kind I was talking about previously about things that don't seem relevant to human performance. The link is tenuous because it is about the practical process of living so it is about the journey. I am now a father and so treating the injuries of others is important as my own. I know that I won't be the only person with this problem. Fixing it helps me get on with my day and my son with his.

I signed up to to make it easier to help my son progress. I asked my wife for the best site and she finds their daily email pretty much spot on. They mention tantrums, he suddenly starts doing them.

So this mornings mail mentioned nappy rash. Their blurb was:
So the next time your baby's bottom breaks out, don't waste time (and money) testing out cream after cream on your own. Check our list to see which skin solutions other moms swear by to find a remedy that really works

Their list seems ok but I had to share what saved the day last year when the nappy rash just would not go away. We tried everything, nappy off all morning, all sorts of creams(bepanthen, sudocream, Canesten HC). You name it. A quick call to our nursery solved it. Metanium. We just use the nappy rash ointment. His bum went from red raw to fine in a day or two and it stopped the pain almost instantly. It's so think you can really tell its creating a solid barrier. Since then we haven't had a problem. We just use the normal barrier creams if we ever have a problem saving this for the heavy duty sore spots if they develop. Haven't had to use it much but its a life save when you do.

We just picked it up from tescos but the sell it at Boots and the discussion on netmums seems to reflect the experience we had. It may not work for everyone but if your little one is in agony, like mine was then it really can save the day.

HTH. If anyone has any better advice then please let me know.

Thursday, 9 January 2014

Future vision for my blogs: New year, renewed focus

The point of this blog is partly to help me raise my son. My vision has always been that by improving my knowledge and experience of human performance and using this to achieve my own dreams I would then be able to help my son achieve his dreams too.

That's the overall vision I have and so far it's been a good choice. Recently I have started to understand what part my blogs can play in achieving this vision.

I thought I would share my vision because I will be posting more things that may not initially seem relevant. It should all make sense in the longer term but I thought I would give you a heads up first. Feel free to skip it if you don't think it's relevant. I just have so many roles these days that I can't be relevant to all people all the time.

Colchambers: Human Performance

This blog colchambers is quite general in its focus. I have many lifelong dreams and many much shorter pursuits which all feed in. The idea is that is my life journey. As well as learning about the body myself I'm looking at ways of expressing what I know as best I can. This means looking into newer technologies like 3d  and virtual worlds, html development tools and wearable technology to name just a few.

Some of what I share will just be tips. I learn so much from little things other people share so I like to give back too. So while some of it may not seem obviously helpful it will still reflect part of my journey. Over time I hope to pull more and more of the content together into an organised whole.

Being a Dad is a huge and fun part of my life but something I haven't shared much of yet. I see that starting to change. I see the role of being a dad as very much like being a coach. A supporting role helping my son get to grips with the world and find his part in it. Much of the role though covers very mundane things. So some posts may cover these things. Apologies but it's a great way to get help and a great way to share useful tips.

The Competitive Urge

the competitive urge explores the impact of competition in our lives. It began as a Tennis blog where I can use my sports science training but I now see it having a much wider focus including education, work, even politics. The urge to compete is everywhere because evolution is everywhere.

I keep noticing that to compete better in tennis it helps to have a wider knowledge of life. Learn from the competition that is going on elsewhere, in other sports and industries. Instead of reinventing the wheel reinterpret the solution from another industry into tennis. For example I think the womens tennis tour could learn a lot from womens gymnastics. That is a sport where the women are the main draw, the men come second.

Cell Your Sole

cell your sole is a science blog looking at how understanding your body can improve your health with a particular focus on the benefits of activity. It covers biology, psychology, chemistry, sociology and more specific topics like genomics. I'm currently working through a series of posts covering the common illnesses that physical activity can help with including obesity, insulin resistance, migrainediabetes and heart disease and alzhiemers and dementia. I am also currently running a series of posts exploring how to lose weight.

Wednesday, 8 January 2014

Fit for daily life

Another example of being fit making daily life easier is when I popped out for a walk around a local lake with some friends and their kids. I noticed how important fitness was. I was carrying one of the kids most of the way. It felt much like doing squats, presses and arm curls all combined.

My five sets of tennis really helped with stamina. It's built up my shoulders very well. It also helped yesterday when I was doing some DIY.

Basically lots of daily things work better when you're fit enough. So life becomes much easier when you're fit.

My idea with these posts is simply so explain why I care so much about being active. It isn't about living longer or even losing weight. It's about having more fun, really living your life. Being fit simply allows you to live your life to the full much more. That can't be a bad thing can it.

Tuesday, 7 January 2014

Are Wearables ready yet?

I've been waiting for wearables for years now. I'm hearing a lot about them recently so I'm wondering if there are any worth getting. I thought I'd start a post to log what I find.

I was inspired by an article in wired,com Wearables Pioneer: How Wearing Tech on Our Bodies Actually Helps It Get Out of Our Way.

engadget wearables

Some I hadn't realised that qualified
  • jawbone up
  • fitbit, flex etc

The hyped ones

Monday, 6 January 2014

Fit for days out: Fit means fun part two

After all this we had to watch the diving and then get home. Here is the list of what we had to do:

  • I used binoculars but this tired my eyes out. Meaning my brain was getting tired from the day and from trying to watch even though the diving only lasted 1 hour. 
  • walk back down the stairs to the exit 
  • Walk to find water water. 
  • Walk out of the aquatic park 15 mins 
  • walk to Stratford 30 mins. 
  • Train to St Pancras.
  • Walk to Euston 15 mins
  • walk to train 5 mins. Walk
  • up platform and over to car 10 mins. 
  • Drive home.

Bloody knackered, I'm 70 kgs (About 12 stone). I couldn't help but wonder how would that feel for someone heavier like 100 kgs.

We loved every minute of it and would happily do it again but it goes to show that doing fun things is a lot of work. The story is similar no matter what fun you do. A trip to the Good food show is just as tiring, so is visiting a childrens play park with our son. So preparing for it in your daily life actually makes sense.

That is why playing tennis during lunch is so useful to me. I play with quite a competitive group so I get quite a work out. Like I say, some times we meet up outside work and have a proper 5 set match. A lot of fun but something you really need to prepare for.  All the running, stopping turning, jumping and everything else over several hours while at the same time having limited food and water and experiencing sun, rain or whatever is actually great preparation for fun days out. Mainly because to my body it's the same thing. It doesn't know the difference, all it knows is that it may not get enough water for several hours, then binge on salty dehydrating food and do a lot of walking.  Oh and of course have lots of drinks that aren't very hydrating like coke or milkshakes. That's part of a fun day out isn't it. It's not so much fun if you avoid them.

I assume this sounds familiar to you because its pretty much the standard food for a day out isn't it. The point is that because I play sport I have trained my body to handle all this in its stride. So I wasn't as tired the day after we saw the diving for two reasons. It didn't take as much out of me as it did everyone else and I recover faster because that is what sports teach your body to do. Replace what has been lost and fix what has been broken.

Boy it helps to be fit

So you've heard my way to make busy days easier to handle. How do you find your fitness helps when you have fun?

Sunday, 5 January 2014

Fit for days out: Fit means fun part one

A theme running through this blog is the idea of Life as play. Make the play in your life keep you healthy. This post comes from notes I made when I took my family to visit the 2012 London Olympics. What I keep noticing through life is that the really fun stuff takes a lot out of you. That's great but it stands to reason that the fitter you are the more fun you can have without breaking or the less the fun will take out of you. Either way its worth getting fit so you can have more fun. I don't hear many people talking about things this way so I thought I would share.

We are just coming home from the olympics and I am writing this on the train. We had a fantastic time and boy am I glad I'm fit. I have built up the ability to play 5 sets of tennis when needed and it made the day so much easier.

What you forget about these days out is the amount of walking, carrying, climbing and general movement you do. You really use your body a lot and even waiting around is tiring. So the day out is always physically, mentally and emotionally draining. You have a great time but you're exhausted by the end.

I like sports because they train you in all these aspects. So does movement in general. I'll run you through how tiring the day was and then how being active helped.

We had tickets to see the diving at the stratford olympic park. Sounds simple enough. Just hop on a train and go watch. Of course that wasn't the case. It never is, particularly when you visit London. Here is the list of things we had to do to get there:

To watch the diving we

  • parked the car near milton keynes train station
  • walked to the station 
  • walked to the platform 
  • almost had to stand on the train. 
  • Walked to kings cross. 
  • Walked to board Javelin train to stratford. 
  • Walked across the park for 50 mins getting free water, and food and finding the park live event to pass the time waiting for the diving. 
  • walk 15 mins to the olympic shop.
  •  40 mins standing in long queue
  •  walked around the shop for 1 hour
  • 30 minutes walking to diving
  • walk up 15 flights of stairs
  • walk to our seats where it was very hot.

You probably think I'm being a bit over the top. I just wanted to show you how many things we had to do that were basically way beyond what we normally do in a day. Parking the car up and walking a short way to work, then walking around work a little is about all we do. Like most people who don't use public transport. So seeing this list makes you realise just how much of a serious effort it is. To cap it off we were really tired for the next day or two because it was so intense.

So how do you find days out like this? Are they are breeze or do they leave you needing a day off?

Check out part two

Thursday, 2 January 2014

Disney movie Frozen and Toddler fun

If you haven't already seen the Walt Disney animated film Frozen with your toddler then you really should. It's the first film we have got through with our little 2 year old. He loved it.

There are so many characters to keep him entertained from a funny snowman called Olaf to a friendly reindeer and a family of trolls. That's just a few.

We also really liked the songs. My favourite is "Let it go" sung by Idina Menzel. I had no idea but she is an internationally recognised singer. You can tell when she really lets rip.

Then there is "For the first time in forever"

Here is Kristen Bell who plays the main character Anna to tell you more about the film.

Of course he got a little tired throught the film but the great thing is that he just wants to lay on you and cuddle. That's kinda easy in the cinema. Oh, and our little on is chatty. So the audience laughed a bunch of times when he commented on and laughed at the film. "Daddy, snowman has nose Ha, Ha, Ha"

Tons of fun :-)

Let me know if you went to see it and how it went. Did your little one like it too?

Related News