CrimsonBase News

Huge Holiday Savings, Alignments and Linux Beta

2010-12-16T15:39:00.007+01:00

The office is buzzing with activity today as we have a number of big announcements to make.

In celebration of the holiday season and today's major update, QuickGene is available for only €50 or $65! That's a €245 or $350 discount and our holiday gift to molecular biologists around the world.

Click here to pick it up before the sale ends!

Sales are limited to three per person, so give it to your boss, surprise the new grad student and keep one for yourself - everyone loves friendly software!

Alignments

We are proud to present to you the next major expansion of QuickGene's capabilities: alignments! As of today, you can easily align any genetic sequences in a project.

Perform both pairwise and multiple alignments.

Choose from the ClustalW, Smith-Waterman or Needleman-Wunsch algorithms.

Alignments are automatically stored in the current project file.

Continue working while an alignment is processed in the background.

Quickly spot and navigate to differences throughout the alignment with the intuitive alignment bar.

We have much more planned for alignments. As usual, you can expect to see many innovative, time-saving additions in coming updates.

Linux Beta

We are also happy to announce the long-awaited introduction of QuickGene for Linux. This is currently in a beta-testing stage, so if you are interested in testing on Linux, please don't hesitate to contact us!

Update 1.3

Naturally, this update has the usual extensive list of improvements, which you can read below.

Other Changes

Added basic support for ABI files

The side-bar is now collapsible to make more space for the sequence view. This particularly increases usability on netbooks.

Faster load times for all systems with extra optimizations for multi-core machines.

Downloading updates now displays a progress bar.

Clicking in the sequence editor to give it focus no longer results in losing a previously made selection. The color of the rulers now also become grey or blue to indicate the focus of the editor.

Searching now fully supports RNA and matches DNA without the need to transcribe.

Fixes

Double-clicking projects in the welcome screen no longer causes QuickGene to attempt to open it twice, causing an error.

Quickly switching options in the statistics view no longer allows the incorrect enzyme list to display.

Activation failure now displays useful error messages.

QuickGene will no longer crash due to broken activation.

Translations are now displayed correctly in RNA sequences.

Fixed various minor memory leaks.

BIOTECHNICA: Two Days in Hanover

2010-10-01T17:38:00.001+02:00

We've only just gotten back from Het Instrument in Amsterdam, and we're heading to Hanover for BIOTECHNICA. Drop by and visit us at Hall 9, Stand D03!

Representatives from GC Biotech and Eric Lammertsma (from Wednesday afternoon) will be at the stand to answer any questions. We're more than happy to give you a demo and show you how easy QuickGene is to use.

Here's a photo impression of last week:

Het Instrument & BIOTECHNICA

2010-09-21T16:33:00.007+02:00

At CrimsonBase we're making our convention debut this year at Het Instrument. We're very excited to be exhibiting QuickGene between the household names in biomedical research, including our friends at Thermo, Bio-Rad, Sigma-Aldrich, Promega, Eppendorf, Fermentas and many more.

We're partnering with GC biotech who are kind enough to share their stands with us. You'll be able to find us from Tuesday to Friday at hall 1, booth B137. Drop by for a cup of coffee, or cocktails and music in the evening!

The following week, from October 6th, you'll also see us at BIOTECHNICA: hall 9, stand D03.

Is CrimsonBase the Next Star of Utrecht?

2010-09-20T16:05:00.005+02:00

Once again, our efforts to make lab-life easier and cheaper have been recognized! Following our runner-up position earlier this year for the most promising innovative Dutch IT company, we were pleasantly surprised with the news that we have just been selected as one of the three nominees for the biannual Star of Utrecht award!

The prestigious title of "Utrechtse Ster" (Dutch) is given to Utrecht's most promising and successful company rooted in science. Naturally, this is right up the CrimsonBase alley, as everyone working in our office is a scientist making products solely for scientists. To top it off, the honorary title comes with a very motivating €2,500 prize.

We're very honored to be nominated, one reason being that the involved organizations and jury members couldn't get any better. This innovation prize is awarded by the Chamber of Commerce (Kamer van Koophandel), Utrecht Innovation Taskforce (Taskforce Innovatie Regio Utrecht), Utrecht University and the foundation "Vrienden van Sonnenborgh" with sponsoring by Rabobank.

To read more about the award and the jury members (in Dutch), visit the website. We will keep our fingers crossed and look forward to the ceremony on the 8th of November!

QuickGene Update 1.2 - Smart lists are here!

2010-07-26T13:45:00.001+02:00

The whiteboard in the office had been accumulating a "top 10" of bugs over the past weeks, and with QuickGene 1.2 we've had the opportunity to mark them as fixed — most of them reported by you! But that's not all that's new with the latest version of QuickGene.

Upon reviewing user feedback, we noticed that there was an overwhelming demand for Smart Lists. The Enzyme Manager now allows you to construct lists of enzymes dynamically by selecting various properties, including the producer, optimal reaction temperature or the maximum number of cuts in the current sequence. Whenever any of the properties change, the lists are automatically updated: a genuinely smart way of managing enzyme lists!

A feature request last month described saving maps in high resolution or as vector files, such as Scaled Vector Graphics (SVG). It is now possible to specify the dimensions or DPI of PNG, JPEG, BMP, GIF and SVG files.

New features

Smart lists allow you to create dynamic lists of enzymes by selecting desired properties, such as optimal reaction temperature or the maximum number of cuts in the current sequence.

A new dialog provides you with more control over the way your maps are saved as image files, and now includes support for scalable vector graphics (SVG).

Changes

The lists of isoschizomers and compatible ends now show more information when clicked.

Sequence tabs have a context menu to facilitate adding, renaming and removing sequences.

Added user feedback while populating statistics table.

Added a search box to the help pages.

Solved problems

GenBank and Fasta files saved with optional QuickGene information could not be loaded in QuickGene.

Recognition sequence could appear incorrectly when spanned over multiple lines.

Connecting to the CrimsonBase server could prematurely timeout when checking for updates.

Information icon was missing in enzyme tooltip.

When searching, features would sometimes turn into search results or vice-versa.

Features wouldn't show in map view when the label didn't fit.

Tooltip in map view remained persistent.

Some specific character entries could corrupt an XML file.

QGProjects wouldn't load if their name was less than 10 characters long.

View options were not scrollable on small screens.

Free QuickGene Webinar

2010-06-04T16:21:00.010+02:00

We're happy to invite you to our first open QuickGene webinar! For a link to register for free, see below.

Our own Eric Lammertsma will be giving a free webinar on Tuesday, June 8th, sketching the situation in molecular biology today, where laboratory tools are becoming increasingly useful and impressive, while development of the software available to researchers seems to have frozen in the '90s.

This is the platform from which the development of QuickGene was launched, finally providing researchers with the usability we have come to expect from software in 2010. Eric will be highlighting how QuickGene continues to strive toward this goal, reviewing its most innovative features, how it can save you time and how incredibly easy it is to learn and work with. He will also be unveiling the upcoming "Smart Lists" feature, which will finally make paper enzyme catalogs completely irrelevant!

The agenda includes:

A short introduction and sketch of today’s lab

The status of current DNA analysis products

QuickGene’s modernized features:
- Intuitive interface and mapping tool
- Robust, easy-to-use search engine
- One-click melting temperatures and weights
- Instant statistics & cleavage tables
- Optimal reaction conditions for all enzymes
- Unveiling of the upcoming "Smart Lists" feature

A review of the included free monthly updates, features and support

The webinar is being hosted by Micronic North America on Tuesday, June 8th at 2PM EST. To register, simply sign up at http://www.micronicna.com/Webinars.html

See you there!

QuickGene Update 1.1 - Introducing Methylation Warnings

2010-05-03T15:40:00.001+02:00

This latest update brings you two handy, new features and a plethora of changes and improvements. The smallest of the two features comes in the form of an unobtrusive, little lock in the corner of the sequence (1), which, with a simple click, helps protect your data from being modified while still providing all the useful information you need. No longer will and inadvertent bump on your keyboard knock everything in your file out of frame!

The second feature is the ability to receive full-fledged methylation warnings (2). When enabled, all visible restriction sites that are potentially blocked or inhibited by Dam or Dcm methylation are marked by a red dot. When hovering the cursor over it for extra information, not only is the usual tooltip with optimal reaction conditions and the recognition sequence displayed, but the exact location and sequence of the methylation site is also unveiled. Everyone accidentally forgets about methylation sooner or later, wasting time and costly enzymes and reagents. Now, you can forget about it and let QuickGene keep an eye out for you!

Of course, we've been listening to everyone's feedback and have made many more changes and repairs, such as the ability to save extra data in Fasta files, improved integration with Mac OS X and enhanced compatibility with 64-bit Windows systems. The enzyme manager has also been redesigned in anticipation of an exciting, upcoming feature. More on that next month!

New features

1 Added methylation warnings. Cut sites that are influenced by methylations are now marked with a red dot.

2 Added a button to lock the sequence, preventing accidental changes.

Integrated native Mac interface controls, namely:
- When the loaded project has unsaved changes QuickGene will show a red marker in the Close button.
- The search field now looks and feels like the common Mac search fields.

Added the ability to save sequence- and project-specific data such as descriptions and notes in Fasta and GenBank files.

Redesigned the enzyme list window and implemented the following changes:
- Significant performance improvement.
- More versatile copying and moving enzymes to other lists using the context menu.
- Split enzyme table and info panel into two different views: either the table is visible, or the panel is visible (with enzymes shown in a single column list)
- Copying enzymes from a list to another list by dragging from the grid to the name of the target list now also works on Mac.

Changes

Simplified the problem reporting dialog and added the possibility to attach files.

Improved loading and navigation speed on the statistics tab.

Improved compatibility on 64-bit Windows systems.

Updated the Help content.

Solved problems

Recognition sites weren't properly displayed across the first and last base pairs in circular sequences.

When copying and pasting the reverse strand or the reverse complement, the features were positioned incorrectly and would point in the wrong direction.

Active search results could be edited, causing various problems.

Active search results weren't updated when the sequence was edited.

The updater could, in some cases, require administrator privileges under Windows Vista/7 and QuickGene would fail to prompt for UAC.

RNA sequences would display the complement as a DNA strand.

Using an & character in the description or name of a sequence or project could corrupt the project file.

Maps saved as image files would show rough edges that were not visible in the map view itself.

QuickGene could fail to start in rare cases when JVM and SWT library platforms did not match.

Dutch Bioinformatics Start-Up Partners with American Distributor

2010-04-28T16:33:00.000+02:00

The young, Dutch bioinformatics company, CrimsonBase, announced today that it has closed a distribution agreement for its DNA research and analysis software. The deal forms a partnership with master distributor Micronic North America for distribution in North and South America.

The software, named QuickGene, uses modern design principles to enable faster DNA research and analysis and prevent potential mistakes. By automating common tasks and packing in major usability enhancements, the time and money spent on basic genetic research is reduced dramatically.

The partnership for distribution in North and South America was closed with Micronic North America, a laboratory equipment distributor and a leader in innovative biological and medical sample storage solutions. With this move, the Pennsylvania-based distributor has expanded its product line to include usability-focused software for molecular biology.

The quick recognition from the United States comes as a welcome surprise. "We have only just begun seeking sales partners and things immediately started moving very quickly. The enthusiasm we're encountering is great and we're excited to be working with Micronic N.A.", said CrimsonBase CEO, Eric Lammertsma.

"The software that's available to us as researchers is hopelessly outdated, incomplete and difficult to use," he explains. "There is enormous room for improvement." That was the reason for his team of Dutch graduate students to found CrimsonBase and, in collaboration with hundreds of researchers around the world, to introduce user-friendly software for genetic research.

The partnership makes Micronic N.A. the master distributor and primary contact for sales of QuickGene in both North and South America. The new software is expected to become available through licensed Micronic N.A. distributors in the coming weeks, but is available in the Netherlands and the rest of the world directly through CrimsonBase's website.

CrimsonBase Hits Top 3 in Dutch ICT Sector

2010-03-19T14:24:00.006+01:00

Yesterday, CrimsonBase became the first company in the life-sciences to attain a position as one of the top three young ICT companies in the Netherlands. This achievement is particularly noteworthy due to the well represented mobile technology and social media sectors, which have a much larger following as popular fields.

At the annual ICTDelta event, visitors, including students, politicians, investors, and entrepreneurs, could both show their support for any of the twenty nominated companies and vote to award a motivational cash prize to one. The prize was awarded to Meetingspot, which facilitates fast and easy organization of events, although CrimsonBase firmly held the largest number of supporters throughout the event.

During her concluding speech, European Union Digital Agenda Commissioner and former Competition Commissioner, Neelie Kroes, invited the top three to meet in Brussels. This honor clearly stood out as the crowning achievement of the proud winners, who will have the unique opportunity to discuss the role of the European Union in the needs of ICT start-ups.

CrimsonBase Scores Big on Innovation

2010-03-15T12:20:00.004+01:00

In the weeks following the launch of its DNA analysis software, CrimsonBase is being thrust toward the spotlight. Having achieved backing from Shell's LiveWIRE program as one of the 200 selected "technostarters" as well as a nomination for the Innovation Top 100 (Dutch) by Syntens, the company is on the brink of enjoying explosive growth thanks to its rapidly expanding network.

CrimsonBase has also been selected as one of Holland's 20 most promising, innovative ICT companies by ICTRegie and will be presenting their products at the prestigious ICTDelta Convention (Dutch) in Rotterdam this week. The annual convention will take place on March 18th at the Rotterdam WTC Convention Center, where admission is free and visitors will be able to cast votes to award the most promising company €10,000. The nomination of the bioinformatics company is particularly surprising, noting the broad scope of the convention, including popular fields such as gaming, 3D technology, and databases.

The product which has attracted so much attention is DNA analysis software, "QuickGene"; a name which, according to co-founder and president, Eric Lammertsma, "perfectly captures our focus. There's no shortage of software in genetics, but there is a stunning absence of user-friendliness and understanding of what researchers need. That's what we're bringing to the table, using innovative approaches to get time-consuming work done quickly and easily." In a recent interview for the Dutch financial newspaper "Het Financieele Dagblad" (Dutch), he stated that over 400 researchers from fifteen countries participated in the testing and development of the software; a staggering response for a small company in such a niche market.

These recent nominations and the enthusiasm of researchers confirm the company's vision. "It's absolutely great and an affirmation that we're on the right track. It's extremely motivating."

QuickGene Update 1.0.1

2010-02-22T13:56:00.006+01:00

The first update after big QuickGene's release, just over a month ago, introduces some smaller changes and improvements. The most popular request was the ability to disable translation of the complement strand, which has been added as a view option. The enzyme database has also received a major overhaul, including the extensive changes to the New England Biolabs buffer recommendations and introducing the EcoRI buffer activities for all NEB enzymes.

Another useful new function is the intelligent annotation of features when opening GenBank files. You have likely encountered the problem of opening annotated GenBank files only to see all the features named "CDS" or "gene". This is common for files that have been saved or modified in programs that save the name incorrectly. QuickGene uses the correct names and, when these can't be found, deduces names from other specifications of features, attempting to provide you with the most descriptive annotations possible.

In the meantime, some bigger, research-enhancing features are approaching completion which you can expect to see next month's update. Stay tuned!

New features

In-line search results can now easily be converted to features by double-clicking on them.

Translation of the complement strand can now be disabled in the view options.

Changes

Updated the enzyme database, including major changes to the NEB buffer activities and recommendations.

Improved security and reliability when activating and updating QuickGene.

Updating QuickGene now shows its progress.

Improved naming of features when opening GenBank files.

Fixed the base pair location in the status bar to update when clicking on enzyme tooltips.

Fixed certain cases where composite features could cause problems in QGProject files.

QuickGene 1.0 Launched!

2010-01-15T15:06:00.000+01:00

Today's the big day! Twenty-two months after starting development, seventeen months after founding CrimsonBase and 365 days after QuickGene's first careful steps into the world, we're very proud to take the "beta" sticker off, making QuickGene 1.0 a fact.

This important milestone was reached thanks to the coordinated efforts of the entire team and in no small part to the hundreds of beta testers who offered constant encouragement and over 500 ideas. All those suggestions have proved invaluable, constantly reshaping and perfecting our plans, and we certainly aim to continue and expand this collaboration. We are incredibly grateful for all their help and to all those who share our ambitious vision of the future of molecular biology, sticking with us as QuickGene's capabilities continue to grow.

The office is overflowing with creativity as we continue to plan better, faster and more intuitive ways to approach common problems and introducing biology to modern software. Needless to say, 2010 will be packed with some of the most innovative updates to date!

Note that with today's release of the first commercially available version of QuickGene, it is also the last day to get licenses at a 25% discount. Hurry to the online store or send us an email if you haven't done so yet! As usual, you can see the complete list of changes and improvements since last week's 0.9 beta update attached below.

The feeling of excitement and anticipation is palpable, but today is reserved for some well-deserved partying. If you're in the neighborhood of the Kruyt building in Utrecht, we invite you to come by our office for some cake! We hope you enjoy using QuickGene as much as we enjoy building it and hope to continue our collaboration in 2010!

All the best,
Eric Lammertsma and the rest of the team

Changes

The in-line statistics calculator is completely restyled. It is faster, can be minimized and can be moved anywhere to stay out of the way of your sequence.

Enzymes in the enzyme manager can now quickly be found by typing the first few letters.

Which translation frames are displayed is now stored for each sequence instead of as a global setting.

Features are now shown with the exact color you select, instead of in a pastel tint, making similar colors more distinct.

Creating PDF files from maps displays feature colors as solid colors instead of as a semitransparent mesh.

Feature names in sequences are now larger and more legible on Mac.

Improved system integration for Windows Vista and Windows 7.

Fixed: The in-line statistics calculator is no longer cut off in short sequences.

Fixed: Search results display correctly in the map views.

Fixed: Search results now report the correct position in their names.

Fixed: Importing or pasting from the clipboard no longer corrupts the complement strand.

Fixed: Removing enzymes from enzyme lists no longer results in those enzymes still being displayed until the list is refreshed.

Fixed: The cursor position and selection in the status bar now correctly display the current setting instead of defaulting back to base pairs when opening a file.

Fixed: QuickGene now displays correctly on computers with non-standard DPI settings.

Fixed: Clicking on enzymes in the circular map now always places the cursor at the cleavage site.

QuickGene Beta 0.9 - Setting the Stage for 1.0

2010-01-06T14:58:00.008+01:00

One week before QuickGene's graduation from beta, launching it into the world for all to use, we're setting the stage with the final beta update. Update 0.9 kicks off the new year with a tweak or two and smooths out a handful of little wrinkles. With this update, it is now possible to activate your copy of QuickGene using a pre-launch license key.

This also means that there is only one week left to take advantage of our deal for beta testers. If you haven't done so yet, hurry over to the store to grab a license for yourself or your lab at a 25% discount!

The modest list of changes in this update is below:

Changes

Added flexibility to the feature creation dialog when handling bookmarks.

Fixed several small glitches in the map view.

Fixed a problem where the view options panel was blank after creating a new project.

Fixed a problem with whitespace removal when copying and pasting sequences which corrupted the complement strand.

Fixed the feature creation dialog not being displayed if the sequence was not selected.

QuickGene Beta 0.8 Delivers User Requested Features and Changes

2009-12-09T16:40:00.012+01:00

As promised, in this update we have focused exclusively on features and changes that have been requested often or by paying customers. In particular, by popular request, we have made navigating to specific positions or selecting regions in a sequence incredibly easy. Simply click on the numbered position, displayed below the sequence, and enter a number or a range in either base pairs or amino acids in any reading frame! Furthermore, the size of a selection can also be changed easily by editing the size attribute. This tool makes exact sequence navigation extremely fast and intuitive.

Highlighting of identical enzyme cleavage sites in maps was introduced in the previous update, but naturally this is also useful when editing your sequence. Therefore, we have added the same restriction site highlighting in the feature bar, next to the scroll bar. This allows you to view all instances of the selected restriction enzyme's cleavage sites without the need to switch to the map, making restriction mapping even easier.

Usability has also been improved by allowing more view customization. For example, the in-line statistics calculator, enzyme information and reading frame highlighting can now be toggled on and off easily. As usual, we fixed any errors people have encountered and this remains our top priority.

Notably, there will probably not be a version 0.9 before the release of version 1.0 and the end of the beta on January 15th. This also means that there is only one month left to grab QuickGene at a 25% discount! With the holidays in between, it will be gone before you know it, so don't miss out!

You can check out the full list of changes below:

New features

Cursor position and selected range in statusbar are now editable in both base pair and amino acid positions.

When hovering over an enzyme in the sequence or map view, the feature bar highlights all cleavage site occurences.

Added support for importing DNA Strider 1.4 files.

Added easily accessible "copy reverse complement" function when right-clicking on a sequence.

Added checkboxes to the view options to allow disabling several display features, such as selection statistics, enzyme information and reading frame highlighting.

Changes

Double clicking a feature in the map view now opens the feature edit dialog.

Added support for Shift+clicking on features in the sequence view to include them in existing selections.

Tweaked and renamed numerous interface elements and features to be more intuitive or easier to access.

Fixed a rare problem in which the sequence would be drawn over enzyme information.

Fixed Mac menu items mistakenly displaying keyboard shortcuts as "Ctrl+..." instead of "Cmd+..."

Fixed rare font problems on Windows computers, resulting in translations and/or the sequence being displayed as nonsense.

Fixed a problem where clicking features in the editor did not select the sequence correctly.

Fixed a problem with reversed features so that they are now copied and pasted correctly.

Fixed the feature creation window where pressing Enter would ignore the properties specified by the user.

Online Store Grand Opening

2009-11-05T11:04:00.002+01:00

We're proud to announce that we have opened our online shop! Today, after 21 months of hard work, we have started accepting pre-orders at a substantial discount of 25%. This is our way of thanking everyone for their support.

This discount will only be available during the remainder of the beta period, which is currently scheduled to last until January 15th with the launch of QuickGene 1.0. Until then, we will be putting extra effort into working out the kinks and making QuickGene smoother and faster.

Ordering a license early also has a number of major advantages:

The price is permanent. Even when the discount ends or if the price goes up in the future, you get to renew your license for the same price every year (with the exception of inflation and exchange rates). That's the price you agreed to and that's the price you keep.

You get a stronger voice. If you need functionality that is missing from QuickGene, tell us! We read and discuss every bit of feedback, but as a paying customer, we owe it to you to listen to your needs first.

You contribute to development. Every penny that comes in goes straight into building better software. This means we can hire smart developers, outstanding designers and enthusiastic scientists that can whip up elegant solutions to every problem we tackle. You're not just paying to use QuickGene; you're ensuring that it keeps getting better.

Of course, development won't stop with the end of the beta. We will continue to pump out frequent free updates, containing slick new features and improvements, with the same enthusiasm you have come to expect from us. We have countless ambitious plans for QuickGene's future and your ideas will continue to be the driving force!

New Website Launched

2009-10-23T17:43:00.004+02:00

After about a month of designing, programming, screenshot taking, writing and rewriting, we have launched the new website! It's a huge improvement over the previous site (seen below) in every way possible. The beautiful, slick design was made possible by the very cheerful and charming Thifane Albuquerque, who donated her talents to our cause.

Naturally, you can surf around and discover it yourself, but the improvements are immense. The site now boasts an extensive support section, which answers the questions we receive most frequently, a very informative list of QuickGene's most advantageous features, some fancy screenshots, more information about the core team and a very nifty contact form. We've been happy to hear your compliments on it! If you're missing any information at all or run into any mistakes, please use the contact form and let us know.

You'll also notice that there's a store underway, which we plan to unveil very soon. Of course, it will be equally beautiful, friendly and easy to use. Check back soon to see the grand opening!

QuickGene Beta 0.7 Brings You an In-line Calculator and Cleaner Maps

2009-10-21T15:21:00.005+02:00

The latest QuickGene update, released today, bumps the version number up to 0.7 and brings with it the customary list of improvements and additions. Most notably, we have introduced an in-line calculator that calculates the molecular weight and melting temperature of any selected sequence. This happens on-the-fly, while you make the selection, helping you create the perfect primers! This is our first step toward primer design and PCR tools and you can certainly expect more to come.

In the meantime, we continue to improve the cloning tools and have made some major changes to the maps. The design is cleaner and more organized and label placement is much more logical. Furthermore, we have added the often requested enzyme highlighting function. Holding the mouse over any enzyme in a map now not only displays its information but also highlights all other occurrences of that enzyme's recognition site. The first speed optimizations have also been added, making map navigation smoother and more useful. We will continue to add speed optimizations in the coming updates.

The full list of changes in the 0.7 update is as follows:

New features

Replaced design for the linear and circular maps, reducing clutter and improving readability and performance.

Added highlighting of all occurrences of a restriction enzyme cleavage site when hovering the mouse pointer over one in the maps.

Added a quick overview of statistical information, including melting temperature and molecular weight, when selecting a range in the editor.

Added cursor position indicator to map views.

Changes

Improved stability on Windows 7.

Improved integration into Mac OS X.

Changed label positioning in maps to be more logical.

Added first speed optimizations to the map view.

Added file-type support and opening QuickGene from Finder for Mac OS X.

Fixed QuickGene being killed when pressing Command + Q on Mac OS X. This now shuts it down neatly, requesting to save if unsaved changes are present.

Fixed the cursor being placed incorrectly when clicking on an enzyme in a sequence. It is now placed at the cleavage site.

Fixed freezes when sorting features in the sidebar.

Fixed the problem in Mac OS X when opening a project from Finder would cause an open project to be closed.

Fixed the problem that translation view options were not remembered correctly between sessions.

QuickGene Beta 0.6 - Even More Reliable and Supporting Windows 7

2009-09-14T11:54:00.004+02:00

Currently, we're focusing on the stability and reliability of QuickGene. When designing your cloning strategy, you want to know the program you're using isn't going to fall apart and crash moments before you save your work. While we're making good on our promise to be the most reliable program out there, we've already built a backup system to make sure that a crash doesn't mean starting from scratch. If an essential component of QuickGene fails, a safety net is in place that will perform a last-second save of your project. The next time you start QuickGene, it will present you with the backup, letting you get back to work, throw it away or save it for later.

Of course, the ultimate goal is for no one to experience that life-saving backup function. In update 0.6.0, we've ensured Windows 7 compatibility and hammered out a handful of bugs. In particular, file and project support has been vastly improved, yet again, and you'll have the pleasure of knowing it can handle huge projects with thousands of features, millions of bases long. If you have a GenBank file QuickGene can't handle, we want to know about it! You can look forward to support for more file-types in the future too.

As usual, the full list of changes in QuickGene 0.6 is below.

New features

Added compatibility for Windows 7.

Feature names now appear within features in the sequence view, and in a tooltip when hovering the mouse pointer over them.

The "Go to base pair" function now allows selection of a range.

Creating features now supports complex features and ranges. (One feature's position may be specified as "100-200,250-300" which will be displayed as a feature from bp100-300. Later, this will be displayed in more detail, clearly showing gaps.)

Changes

Improved feedback panel in the welcome screen. (Please revote on items that have no yellow stars)

Fixed crashes when importing sequences into a project.

Fixed unnecessary "problem" messages regarding unknown or misplaced keywords when opening GenBank files.

Fixed crashes when rapidly sorting enzyme lists in the Enzyme Manager and Statistics tab.

Fixed importing QuickGene project files (.qgproj) that would result in empty sequences.

Fixed screenshot thumbnails in the feedback dialog being distorted.

Update Addresses Issues Caused by Java 1.6 Update 15

2009-08-10T13:52:00.003+02:00

Sun and Oracle would do well to test and repair their updates as rigorously as we do! Last week, an update was released for Java, the technology on which QuickGene is based. That update contains a major flaw for Windows users, which prevents QuickGene (or any other Java program) from accessing certain essential information it has stored in the registry. This causes QuickGene 0.5 to crash while starting up.

Unfortunately, this update was released at nearly the same time as the QuickGene update, resulting in a number of computers containing the both the new Java version and QuickGene 0.5. Per chance, none of the four PCs in the office had the update, which caused the problem to go unnoticed until we updated our QuickGene installations at home and received reports from beta testers about mysterious crashes. Of course, we got to work on the problem immediately and, two hours later, we released a new update to version 0.5.1. This temporarily circumvented the problem, avoiding further crashes and allowing people to run QuickGene once again, despite the errors in Java.

Today, we have released an improved version which entirely avoids the current registry access problems currently present in Java. All Windows users should check for updates via the "Help" menu or download and install the latest version (currently 0.5.2) as soon as possible.

QuickGene Beta 0.5 Adds Easy Navigation to Vector Maps

2009-08-07T17:29:00.005+02:00

A great deal of work went into the step to QuickGene's update to 0.5, including a complete overhaul of the way in which maps are displayed. Users might recognize the navigation methods from regular map services such as Google Maps, in which smooth scrolling and zooming with intuitive mouse controls were a refreshing innovation. We've adopted this natural feeling navigation method for use in genetic maps, making QuickGene's map controls the most intuitive in existence!

Standard functions such as printing, saving images, toggling the display different elements and many other enhancements have also been added to the map view. This view replaces the previously available linear and circular views, further enhancing the clean, straight-forward interface QuickGene aims for.

One of the most popular requests we receive is the ability to choose which buffers to display, when more than one is available. As always, your wish is our command! Users may now also specify their preferred enzyme supplier in the Enzyme Manager, which will then always display those buffers when available for any given restriction enzyme. This includes the buffers displayed anywhere the Enzyme Manager as well as in tool-tips shown when hovering the mouse over restriction sites in a sequence or map.

Full support for saving files to the GenBank format has also been completed, allowing for extended interaction between QuickGene and any other software tools you use. Furthermore, QuickGene can now open even more file-types and even attempts to recognize sequences in files it doesn't recognize!

We hope you enjoy all the improvements and feel free to give us your opinion.

The full list of changes is as follows:

New features

Sequence maps have been completely rebuilt and now include:
- More intuitive navigation using mouse controls
- New navigation controls and a mini-map
- Ability to print maps and to save maps as image files
- Merged linear and circular maps into a single view
- Added view options to select topology and visibility of features, enzymes and rulers
- Improved map rulers
- Improved display speed
Replaced "Sequence Editor" shelf-menu with more intuitive, view-dependent "View Options"

Added colorized feature icons, indicating bookmark, feature or search result, including direction and strand, if applicable.

Full GenBank support with additional support for QuickGene-specific information, such as colors, non-directional features and bookmarks.

Added the option to select which enzyme producer appears first in tooltips and in the enzyme manager

Added option to copy a selection as the top or bottom strand in either direction or as a translation in any frame.

Changes

Added a warning dialog when saving in the Fasta format when data may be lost

Increased flexibility of opening simple sequence files

Improved loading speeds of enzyme lists

Merged the "Sequence" and "Project" menus, introducing a new "Map" menu for newly introduced functionality

Fixed certain ".seq" files occasionally not being recognized as valid sequences

Fixed rare cases of missed enzyme cleavage sites with ambiguous, palindromic recognition sequences

Fixed incorrect and inconsistent frames of translations

Fixed display of bookmarks in the sequence editor

Fixed available space in the status bar for base position and selection sizes

Fixed base number of cursor position to be more logical

Fixed printing sequence with single-letter translations

Fixed printing sequence with features

Testing Period of QuickGene Extended Through Summer

2009-06-25T16:22:00.002+02:00

Following all the great feedback we've been receiving, we would like to thank all our users for all their help and have decided to extend the test-period throughout the summer months! Thanks to you, QuickGene is growing rapidly and constantly becoming faster and more robust.

To extend the testing period of QuickGene, it needs to be updated to the latest version, 0.4.2, before July 1st!

You can do this easily by starting up QuickGene and, if it does not begin updating on it's own, selecting "Check for updates" in the help menu. If you have a version older than 0.3, you will need to download the newest installer from http://www.crimsonbase.com/download using the email address you signed up with. After installing, follow the same steps to perform the update. You can check which version you have by selecting "About QuickGene" in the help menu.

QuickGene Beta 0.4.1 Improves Large File Support

2009-06-19T17:12:00.003+02:00

The newest update to QuickGene, which just rolled out a few minutes ago, brings with it many behind-the-scenes improvements. The small version number change, from 0.4.0 to 0.4.1, reflects the relatively small number of obvious differences. The first difference will be clear immediately upon opening QuickGene after the update. The welcome screen now allows every user to easily rate popular ideas, letting us know which items are high priority and allowing us to focus on these during development. Additionally, providing new ideas and feedback regarding problems or suggestions has become much easier.

Behind the scenes, and tucked in various corners of QuickGene, are some larger changes. Much focus has been placed on enhanced support for large files, as many users have noted that QuickGene handles files containing over five million bases with ease. We have expanded this support to include massive GenBank files, which may contain tens of thousands of annotated features, and increased performance and loading times. In general, file loading capabilities have also been tweaked for reliability. Drawing maps at these vast sizes is currently not functional, however we have a number of enhancements to the map view coming up soon!

Support for Mac OS X has also been broadened to include 10.4.x, so Tiger users no longer need to feel left out. Another much requested feature has been partially implemented, allowing selection of reading frames for translation as well as selecting single-letter translations. In a future update, annotated features may have a reading frame assigned to them, so that relevant translations can be shown locally, as opposed to throughout the entire sequence.

The full list of changes is as follows:

New features

Added a rating system for popular feedback

Added an option to view single letter translations

Added an option to view only specific reading frames

Changes

Broadened Mac OS X support to include 10.4.x

Greatly enhanced performance for large files

General improvements to file loading

Improved support for malformed GenBank files

Improved display of features next to the scroll bar

Simplified feedback dialog

Increased performance when scrolling

Made general improvements to stability

Fixed: Features are displayed in the correct order

Fixed: Closing projects always returns to the welcome screen

Fixed: Feature colors are saved correctly on Mac

Fixed: Numerous mouse-related bugs in the sequence editor

The next major update will complete support for GenBank files, allowing for saving of sequences according to the exact NCBI specifications. Furthermore, the aforementioned enhancements to the graphic maps will be added, allowing for much more intuitive navigation and additional support for large files. As usual, you can expect a lot more changes soon!

QuickGene Beta 0.4 Released

2009-05-27T11:58:00.003+02:00

Today, we're rolling out another major update which brings with it a list of new features and changes but, most notably, renewed support for Mac OS! Due to a broken development machine, we were unable to keep the Mac version updated and since the arrival of a replacement we've been hard at work, pushing QuickGene's Mac support back up to the most recent version. Mac users will therefore experience quite a difference and we'd love to hear what you think!

Naturally, the update brings more to the table than Mac-only news. The list of changes since QuickGene Beta 0.3 is one we're proud of, introducing much-needed features such as the long-awaited printing capabilities and many improvements to the search function. The full list is as follows:

New features

Updated support for Mac OS X

Sequence Printing

Numerous search options

Search results indicate strand and direction

Amino acid seqence search

Changes

More informative enzyme tooltips

More intuitive searches and results

Removed the need to specify search types

Copying and pasting sequences includes features

Creating screenshots for bug reports can be done at the press of a button

Fixed: Sequence selection is not lost when interacting with enzymes or right-clicking

Fixed: Sequence can be selected between restriction enzyme cleavage sites intuitively

Many smaller repairs and user-requested changes

We're currently working on adding a number of essential functions such as the ability to save in the GenBank format and further expansion of search capabilities, as well as building more of the features you have been requesting. There are truly some great ideas coming in and we can't wait to get to work on them!

Mac Support and Update Preview

2009-05-01T14:07:00.003+02:00

Don't despair! We certainly haven't forgotten our Mac users!

Mac support has been unfortunately delayed, as our development Mac had been sent in for repairs after the 0.2 update and was only recently declared officially deceased. We hope to have a replacement by next week, at which point the available updates can be edited for Mac compatibility and tested for release. We apologize for the inconvenience and we're well aware of the major changes that Mac's are missing out on.

Following this week's update, which featured user-requested changes and repairs, the next update is planned to include more major functionality enhancements. Currently, these include a complete overhaul of the search feature and implementation of the previously announced printing capability.

The search function is currently undergoing a major upgrade which will make it the most robust, intuitive search available in any sequence analysis software. Most importantly, it's smart and straight-forward, allowing users to easily find any sequence, restriction enzyme or translation without the need to tell QuickGene. Furthermore, many useful standard and unique search criteria can be specified when more control or specificity is required. We're confident that you'll be amazed how much more quickly you can zip through your projects, finding exactly what you need.

Although the announced sequence printing functionality is already working, its release has been delayed as we ensure compatibility with most printers. Once this is completed, it will be included in the next update and map printing will be soon to follow.

Development of QuickGene continues to steam forward and we're having a great time building it, reading your feedback and dreaming up new features. Stay tuned for the release notes of the next update to find out more about it!

QuickGene Beta Update 0.3.1 (PC only)

2009-04-28T10:52:00.002+02:00

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!