QuickGene Beta Update 0.3.1 (PC only)

Update 0.3.1 for QuickGene was released this week, focusing strongly on user-feedback. We addressed a number of problems and made numerous changes to the interface and usability, making many features clearer and easier to access. Most notably, the search function received a small update, which is only a hint of things to come. It now searches both strands by default (the template strand and reverse complement) and will soon receive an update to set these parameters.

The bulk of work for this update has gone into repairs and modifications requested by users. These include the following list of changes:

• Statistics tab now has the option to display non-cutting enzymes.


• The general design has been improved. (Let us know what you think!)


• Restriction site searches are 20% faster.


• Translation readability has been improved.


• Stability and crash detection have been improved.


• Fixed: Searching now includes the reverse complement. (Configuration options will be included in the next update)


• Fixed: Nucleotide counts now update properly after editing the sequence.


• Fixed: GenBank file requirements have been relaxed. (QuickGene now still attempts to open GenBank files that do not adhere exactly to the GenBank specification)

Naturally, we are very committed to building what you need and have been working hard to do so. Keep sending us ideas for improvement and we'll continue adding them!

CrimsonBase Featured in Debut Edition of "De Utrechter"

The new regional weekly paper, "de Utrechter," printed it's debut paper last November, which is now available online. This was distributed to thousands of residents of the beautiful city of Utrecht, which we're proud to call our home. Its cover article features CrimsonBase and co-founder Eric Lammertsma in an article about the city's growth and potential in collaborating businesses and academic institutions. As a company founded and run by graduate students, we made a perfect fit for the article. Below is a short, translated excerpt.

This is the man; the entrepreneurial student that will provide Utrecht with bright perspectives. His name: Eric Lammertsma, founder and CEO of CrimsonBase, a company consisting of four people, but possibly one of the future pillars of Utrecht's economy.

CrimsonBase makes software for DNA analysis and assembly. During his research in the biomedical sciences, Lammertsma (25) became frustrated enough with available software to start working [on a solution] with his brother and a befriended computer scientist. Now, CrimsonBase is one of the start-ups in the Center for Entrepreneurship and Innovation of Utrecht University and the Hogeschool Utrecht, a mouthful for a floor in a concrete, 70's colossus in the Science Park. There, Lammertsma sits at his laptop in his office on brand-new, striped carpet. In the hallway, construction workers add the finishing touches to the wiring and linoleum. After renovation, there will be room for 24 student-entrepreneurs; no logistics services or website designers, but innovative, ambitious businesses.

The two page article goes on to cover other aspects of Utrecht's economic climate with views from politicians, academics and incubators, such as the CvOI, where we are located. We're proud and a bit humbled to be put in such a positive light in the first edition of this new weekly paper. It can be downloaded for free on the site of "de Utrechter."

QuickGene Beta 0.3 Released

We're proud to announce that the next update, 0.3, is now available! Before you run to download it however, please note that if you already have QuickGene, the update will download automatically within the next week. You can also make it update itself now by clicking "Check for updates" in the help menu. If you don't have a copy of QuickGene, you can sign up to beta-test it for free. (We're currently in the process of simplifying this, so you can get your hands on it without waiting for a personal invitation from one of us.)

Version 0.3 boasts two big, new features and a battery of improvements. QuickGene is now faster, smaller and more stable! The first feature you may notice is the addition of in-line translations. Translations are displayed in all three frames of your sequence and, if you view the complement strand, reverse frames are shown, as well. Hovering the mouse over a line of translations highlights them, as well as the corresponding codons, providing a much clearer view. A translation manager has also been built to allow selection of alternate translation tables, easily accessed through the tools menu or by pressing F6.

The second obvious addition to QuickGene is the "Stats" tab, which offers statistics and extra information on the sequence currently in view. Most notably, this new tab contains the often-needed restriction table, which allows you to view how each individual enzyme interacts with your sequence. The table combines all the data you need, allowing you to quickly view unique cutters, fragment sizes, and graphical representations. Furthermore, this tab allows you to quickly edit the sequence's name, circular or linear form, description and notes as well as view nucleotide frequencies and GC-content.

As we continue to work on overall improvements, we're still eager to hear your ideas. Next up are expansion of the feature-types with more design options, expansion of search capabilities, printing functionality and Vector NTI database import. We're also eager to move on to bigger, future improvements such as full AB1-support with editing and alignment capabilities, primer design, contig assembly, and extremely streamlined cloning advice. There's plenty to do so let us know what your preferences are!

CrimsonBase is Growing

As we constantly work on building the friendliest, most time-saving DNA analysis application to date, there's increasingly more to do. Everyone's working more than full-time and yet work is still piling up. Thus, it's clear that we need more people to lighten the load. To this end, we currently have two internship positions that need filling in the areas of web-development and marketing / customer care.

The website needs an overhaul and some major additions as our first product, QuickGene, approaches maturity. We're much too busy working on the latter to make time for website improvements and would like to welcome a student to take on this task.

The second position is much needed in view of QuickGene's increasing popularity as we aim to keep a constant dialog with the scientists we serve. It is truly a product of collaboration and this means we need help in keeping communication up to par as well as conveying our scientist-to-scientist attitude and our level of motivation to make biology software easier to use, saving everyone time and money.

If you're interested in joining our small ambitious bio-tech team, send us an email or give us a call. We'd love to hear from you!