Software Engineering and Bioinformatics

Code-Working is your solution for Software Engineering and Bioinformatics.

Hello, my name is Joachim Beig.

I am a Bioinformatician and Software Engineer. These two fields combine many things I love, like Biology, Databases, Big Data and Data Processing. However, the most important thing for me is to find solutions for problems.

Over the years, I worked in various fields as Web Application Developer (Sony Music Entertainment Germany GmbH, Proteros biostructures GmbH), Bioinformatician (Max Planck Institute of Biochemistry, Helmholtz Zentrum München) and for my own business, where I combine both fields.

Corresponding to my working experience, my skills also grew to a wide variety. I never used specific tools exclusively, but always are looking for simple and straightforward solutions.

However, my main focus is currently on the following tools and techniques:

  • PHP (CakePHP)
  • MariaDB / MySQL
  • Linux / Ubuntu Server
  • DevOps
  • JavaScript (jQuery)
  • OOP Style
  • Regular Expressions

I've also used the following tools with lower experience:

  • CI / CD
  • Java (with Swing)
  • Java EE (with Glassfish Application Server)
  • Perl
  • PostgreSQL

Below you will find a selection of my work:

PPC Rocket

While working for and talking with marketing managers I found out that AdWords is a tricky thing. If you're managing a huge website, it is hard to track every single keyword that currently does not well perform. But this is sheer waste of money!

To help people out of their misery, I co-founded the PPC Rocket GmbH in 2017. The tool developed by us currently consists of four modules:

Quality Score

There are many factors that influences the effective cost per click on an ad. Google combines those factors in its “Quality Score” (QS). The higher the QS of a Keyword, the lower are the effective costs. PPC Rocket analyzes your quality scores and the influencing factors from the keyword level up to an account health report and provides an overview dashboard and detailed report on every level. This allows marketing managers to react quickly on worse performing keywords and ads and save money.

Landing Page

It is known that for online shops the conversion rate approaches zero if the number of available products on a landing page falls below a particular threshold. PPC Rocket allows an automated analysis of the (AdWords) landing pages. It can react automatically with either pausing the corresponding keywords or ads or switching the keywords destination URL to another landing page where enough products are available. Daily reports can - among others - help the purchasing department: they can react quickly on reductions of the number of products on a distinct landing page.

Shop Analytics

Besides the AdWords landing page analysis, PPC Rocket can analyze all URLs from Analytics accounts, too. In a detailed report we display the number of products of a distinct page in combination with the main key performance indicators (KPI) of Analytics.

Performance Reporting

To provide an quick overview of the performance of an AdWords account that can be extended down to a fine-granular level, we are developing a performance reporting tool. The performance reports can be filtered and segmented to provide a very flexible report that can be adapted to our customer’s needs.

You see, PPC Rocket is the perfect tool for marketing managers!


Logfiles provide valuable information about the behaviour of search engine crawlers on a website. But a detailled logfile analysis is very complicated and time-consuming, especially for big websites with huge traffic.

The idea behind crawlOPTIMIZER is to help sophisticated and professional SEO teams to process and analyze their logfiles automatically. The dashboards and reports contain analyses about the (wasted) crawl budget, average crawl rate, business relevant pages and much more. Furthermore, there is a raw logfile explorer as well as a url-based logfile explorer.

As a cooperation between PPC Rocket GmbH and eCom VIKINGS, we are responsible for technical realization of the crawlOPTIMIZER system. The analyses must be fast and scalable, even for very large datasets.

Proteros Databases

What has started as a student project by a friend in 2013 grew to a relatively big project that ran until End of 2017. The aim of this project was to create a mobile-accessible, searchable protein catalog for the Proteros biostructures GmbH.

Besides the very ambitious purpose (for a student project that should take a couple of hours), the requirements specification changed repeatedly over the months and years. But finally, the catalog was published on the Proteros website.

During my work, people from Proteros asked me to help them organizing their projects and data within a single, centralized database as an interim solution until launching their future software. So I created some kind of a LIMS by processing a vast amount of Excel Files containing various data formats, images and so on.

Meanwhile, Proteros has upgraded their website and built their own "search engine" for their product gallery.


As part of my work as bioinformatician at the Helmholtz Zentrum München, I am developed a Labor Information Management System (LIMS) for the European Mouse Mutant Cell Repository (EuMMCR).

EuMMCR is part of the European Conditional Mouse Mutagenesis (EUCOMM) program, which itself is part of the International Knockout Mouse Consortium (IKMC). The goal of IKMC is to mutate all protein coding genes of the well sequenced C57BL/6 mouse cell line in embryonic stem (ES) cells by the combination of gene trapping and gene targeting. The genes are mostly allocated between the Knockout Mouse Project (KOMP) in the USA and EUCOMM in Europe. Thus, the goals for EUCOMM and its follow-up project EUCOMMTools are to create and archive up to 12,000 conditional mutations across the mouse genome in mouse ES cells. EuMMCR, however, is responsible for archiving the produced ES cells and distributing them to the scientific community all over the world.

Which sounds like an easy task at first is not that trivial if it comes to details. In short, the LIMS consists of modules that track the samples in the cryo storage, handle online orders from scientists, manage ES cell expansion in cell culture and quality controls of the DNA and, finally, facilitates the shipments to the scientists.

This said, the EuMMCR LIMS supports the scientists and technicians in the EuMMCR lab and helps optimizing the costs by enhancing the efficiency of the lab.

Besides the LIMS development, I helped developing new possibilities to use the EUCOMM targeting vectors in combination with the CRISPR/CAS technology. Furthermore, I was responsible for the shipments of our probes to scientists all over the world, financial reportings of the daily business and many more small tasks that need to be done.

During my work, some interesting papers got published:

Kaloff, C. & Anastassiadis, K. & Ayadi, A. & Baldock, R. & Beig, J. et al. (2017):
Genome wide conditional mouse knockout resources
Drug Discovery Today: Disease Models 20:3-12
Schick, J.A. & Seisenberger, C. & Beig, J. et al. (2016):
CRISPR-Cas9 enables conditional mutagenesis of challenging loci
Scientific Reports 6:32326

Album Of The Day

Album Of The Day is an app from Sony Music Entertainment that is being used worldwide. It is available for iOS and will be also available for Android soon. Users can buy reduced albums (Deals) from iTunes or Play Music. These deals are only available for 24 hours, so every day a new deal.

My part was to develop the backend for the Sony Music Entertainment Employees, so they can easily manage the deals for one or up to all available countries. The backend is set up on a Croogo CMS that was enhanced by the Sony Music cracks to fit the security guidelines.


Starting in 2006, I’ve developed the MyBackstage community system for Sony Music Entertainment Germany GmbH. The main goal was to create a flexible and scalable community dashboard for artist websites. Until 2012, the system was installed on over 30 artist websites, including Peter Maffay, P!nk, Mario Barth, Andrea Berg, Elvis Presley, Britney Spears and much more, and was used by a large number of active users. On the top of all this, we developed a digital shop system (after all, Sony wanted to sell their music).

We adapted the most common social features from that time. The fans were able to write social news about their artist besides official news. Furthermore, they could find friends, create and join groups, upload photos and videos, write their own blog, other people’s guestbook or private messages and much more. Furthermore, we implemented a chat, a forum and a calendar with official dates and dates from fans.

Everything could be rated and commented, and we tracked the activities of the users to create rankings. Additionally, the users could accomplish missions based on the social activities. Everything was done with the goal to encourage users to be more active.

Facebook became more and more popular over time, while content management and handling privacy issues of the user-generated content got more cost- and work intensive, not at least by the data breach of Sony Playstation in 2011. s a result, the MyBackstage system was replaced by official non-social websites, and the communities migrated to other networks.

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