Profile : mekentosj.com : Software for Research

Design software for research.

We are Mekentosj, an independent software company that writes innovative software for researchers.

It all started way back in 1995 when Tom and Alex both signed up to study Medical Biology at the Free University in Amsterdam. Tom is originally from Twente a region in the east of The Netherlands, while Alex lived in Aalsmeer, a flower city not too far from Amsterdam.

They became good friends pretty soon afterwards. After their study they both ended up at the Netherlands Cancer Institute (NKI) in 2000, where they did their PhDs together.

While doing their PhDs they started building software to address the daily needs in the lab. Soon they realized they were not the only ones who could use those programs and they made them available for free on their website, mekentosj.com. In 2004 they won their first Apple Design Award, followed by two more in the following years. That was when things really started taking off, and the rest is history.

Tom and Alex received their degrees in November 2006, after which Alex moved to Cambridge in the UK for a postdoc at the European Bioinformatics Institute while Tom moved back to Twente for a postdoc at the University of Twente.

While Tom continues to pursue an academic career, Alex decided that what started as Mek&Tosj would become Mekentosj Inc, and he now lives the indie life.

In March 2009 Matt said goodbye to the Wellcome Trust Sanger Institute in Cambridge to join the team to push limits further and create revolutionary new software for scientists. Charles followed in May, giving up his job as Chief Scientist at a Stanford startup to start on a great new adventure.

In March 2010 Matt was recruited by Amazon's web services to build the next revolution in Cloud computing and Mekentosj welcomed two new adventurers to our expedition. Constantine Nicolaou, Matt's long time collaborator from Sanger, joins from Beirut, along with Mark Bate, legendary architect of the largest Xserve cluster in the southern hemisphere, who dials in from Melbourne, Australia.

June 2010 marked the arrival of Finnish-born Matias Piipari, Mekentosj's first full time iOS developer, after a very successful launch of Papers for iPad in April earlier that year.

By designing new and innovative software we aim to make the lives of scientists easier and hope to improve science as a whole.

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The Mekentosj.com Team

Alexander Griekspoor

Founder and CEO

Charles Parnot

Our man in Palo Alto

Mark Bate

Wrestler of crocodiles and infrastructure

Constantine Nicolaou

Code wizard

Matias Piipari

Master of Futuristic Devices

Gerrit Griekspoor

Our Wall Street analyst

The people behind us

Matt Wood

Ruler of the clouds

Tom Groothuis

There from day one

Mathijs Voorhoeve

Beta tester pur sang

Dave Gohara

Junior Sales Assistant

Lennert Janssen

Molecular Biology king

It all started out as a hobby driven by a long-time interest for both design and technology.

I was introduced to the Mac when my dad brought home one of these "portable" classic Macs when I was about 14 years old, and almost immediately I started experimenting with Photoshop et al. During university I earned some money in my spare time by designing and building websites, but it wasn't until about the time I started by PhD that Apple introduced Mac OS X and with it came the free set of developer tools that finally made it easy enough for someone without the classical IT background to start building his/her own Mac applications.

Together with my best friend and fellow PhD student Tom Groothuis we started building a number of tools for molecular biologists, which we distributed for free under our "mek en tosj" monicker. It didn't take long before the hobby started to get out of hand as the popularity of our programs started to soar.

When the time came to pick a postdoc I knew one thing for sure, the programming was something I was so passionate about that it should be part of the postdoc rather than a spare time project. That's why I picked the text mining group at the European Bioinformatics Institute in Cambridge UK, also driven by an interest in the changes that were/are ongoing in the scientific publishing industry. I applied for a two year EU Marie Curie fellowship which I was fortunate to get, however it would take a few months between the end of my PhD and all the bureaucracy before I could get started in Cambridge. This was when I decided to build Papers. I got the idea for this "iTunes for PDF files" already two years earlier, but never had the time to do it. I did tell everybody I knew about it, but no one had done it and now finally I had some spare time on my hands.

The first beta of Papers was released right at the time I started my postdoc and it was a success right from the start. In fact it was so successful and offered so many opportunities that it was soon difficult to focus on my actual postdoc and after a year I realised that this was the thing I was really passionate about and was what I wanted to concentrate fully on. That was when I decided to quit my job and become the company founder of Mekentosj Inc. ;-)

The Mekentosj.com Team

Alexander Griekspoor

Founder and CEO

Matt Wood is an author, developer and lover of obscure Swedish indy music.

Matt’s interests lie in adding value to biological data through scientific software: after completing his PhD, he’s built grid services in Nottingham, web-scale search engines in New York City and genes in Hinxton.

He is always happy to chat about science, software or anything in-between. Feel free to contact him via email or on Twitter.

The Mekentosj.com Team

Matt Wood

Master of Disaster,
Ruler of the Rails

Mark Bate

I became interested in computers at an early age in life. At age 5 I taught myself how to word process on my Dadʼs Amstrad. At age 6 I taught myself how to run games on my Grandadʼs Tandy. For my 8th birthday my parents bought me an Atari 520 STE, on which I taught myself how to program in ST BASIC and STOS, after that there was no going back!

As part of my double Diploma of IT: Software Development / Web Development at Swinburne University of Technology, I spent 6 months working on a project with Associate Professor Ashley Buckle at Monash University in Melbourne, Australia.

After completing my double diploma I joined the Buckle Lab and became the labʼs bioinformatics software developer and system administrator. During this time I began to experiment with “smarter” ways of doing bioinformatics. Thanks to some tutorials from Charles Parnot, I got a hankering for Xgrid, Appleʼs grid technology. I built an Xgrid from the desktop Macs in the lab and quickly started adapting several existing applications as well as developing new ones to take advantage of it.

The Buckle Lab soon discovered itʼs research was fast out-growing the compute resources available to it, so I was put in charge of purchasing, building, installing, configuring and administrating Orchard, an Apple Xserve cluster developed solely to assist and accelerate research into protein structure and function. At 100x 8-core Xserves (800 cores), Orchard is the largest Apple cluster in the Southern Hemisphere.

Iʼve presented several conference sessions & workshops on Xgrid and High-Performance Computing on Mac OS X for Apple University Consortium, through whom I have received several scholarships to attend both the MacWorld & Appleʼs WWDC conference in San Francisco, where I first met the other Mekentosj guys (Alex at ʻ07, Charles at ʻ08, Matt at ʻ09).

My passions are High-Performance Computing, bioinformatics, collaborative research, open data, Ruby and Mac OS X, so when Alex & Matt asked me to come on board as the Australian arm of Mekentosj and run all the infrastructure stuff, I jumped at the opportunity!

Iʼm always happy to chat & offer my opinion on things. Feel free to shoot me an email or catch me on Twitter or FriendFeed.

The Mekentosj.com Team

Mark Bate

Wrestler of crocodiles and infrastructure

Constantine Nicolaou

Marahaba! (that's greetings in Lebanese),

I'm Constantine Nicolaou, a Ruby on Rails developer based in Beirut, Lebanon.

I started drawing complex diagrams on AutoCad R12 using an Intel 864 based PC at the age of 12, (via the command line). I completed a BA in Management Information Systems studies at Haigazian University, Lebanon where I co-founded, designed and published a business and informatics magazine (BE-News).

During my studies and in addition to working as a sys-admin and web developer for Saint Mary's Orthodox College, I started surfcampus.com, an academic social portal for Lebanese students.

I landed in the UK early 2006 and joined a local District Council where I first started using Ruby on Rails. Coming from the world of PHP, Ruby on Rails was love at first sight and I soon became heavily involved in bringing legacy applications to the world of Rails.

In the meantime, at the Wellcome Trust Sanger Institute, I joined Matt Wood's team behind Sequencescape, which formed part of the Institute's next generation sequencing platform. At Sanger, I had the chance to work closely with scientists and talented developers on complex requirements -- specifically, handling and curating large data sets by building and integrating apps and API design.

Interested in emerging technologies, cloud computing, NoSQL movement and DSLs (Domain Specific Languages) I'm huge fan and a loud voice on TDD and BDD (Test and Behavior Driven Development).

My Github profile includes more links and info.

I'm also on:

{ "social": 
    {  
        "twitter": "twitter.com/cnicolaou", 
        "skype": "constantin.nicolaou",
        "linkedin": "linkedin.com/in/cnicolaou"
    }
}

The Mekentosj.com Team

Constantine Nicolaou

Code wizard

Matias Piipari

I am Matias, and I'm an iOS and Mac developer hailing from Cambridge, UK.

Much like the rest of the awesome team at Mekentosj, my passion for writing software for scientists has formed as a combination of working in science, and from a ridiculously long standing interest in computers and programming. I begun my professional career in software at the fresh age of 19 by working as a Java programmer in a new media company close to my home town in Finland, before leaving for London to pursue a biosciences degree at Imperial College. After training as a biochemist, I decided to blend my scientific and computing interests into a computational biology PhD at the Wellcome Trust Sanger Institute.

My interest for programming Cocoa applications was sparked by a data visualisation and management problem which hit me early on during my graduate studies. Soon after I had begun writing a Mac based solution to the problem (iMotifs), the iPhone SDK arrived. This very quickly lead to me becoming a scientist by day and a Cocoa geek by night. Indeed, within months I had teamed up with another Sanger trained biogeek Ben to start developing iPhone software as Pear Computer LLP, and now two years and several iPhone and iPad apps later, I am shamelessly in love with this technology and its potential. However, most of all I am extremely proud to join Mekentosj and take what I've learned to make the lives of scientists easier and more productive by means of kick-ass software.

Apart from Cocoa based technologies, I take a big interest in Java which I've written for a long while, and I'm also well versed in Ruby for general-purpose scripting and for the web (Ruby on Rails). In my free time I like to make loud buzzing noise.

The Mekentosj.com Team

Matias Piipari

Master of Futuristic Devices

Charles Parnot is a mutant scientist recently metamorphosed into a Mac OS X software developer.

During his PhD in Paris and his postdoc at Stanford University, Charles used molecular biology and biophysics to study the activation of G-protein-coupled receptors, a class of membrane proteins particularly relevant for drug development.

He also developed a computational approach to analyze the dynamics of this activation process, and later set up the Xgrid@Stanford cluster to help with the computations. He then spent 4 years as chief scientist at ConfometRx, a biotech startup focusing on G-protein-coupled receptor crystallization, with the goal of accelerating drug design and drug development.

Charles always liked writing Cocoa code in his copious free time and he is the author of GridStuffer and of the GridEZ framework. Recently, he made the jump to full-time developer and joined the Mekentosj family to work on a super-duper top-secret new project in sunny California.

The Mekentosj.com Team

Charles Parnot

Our man in Palo Alto

The Mekentosj Story

Alexander Griekspoor

Charles Parnot

Mark Bate

Constantine Nicolaou

Matias Piipari

Gerrit Griekspoor

Matt Wood

Tom Groothuis

Mathijs Voorhoeve

Dave Gohara

Lennert Janssen

Alexander Griekspoor

Matt Wood

Mark Bate

Constantine Nicolaou

Matias Piipari

Charles Parnot

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