MacVector 11.1 has just been released. You can check out the new features of this release on this blog post or a fuller list is available here.
Existing customers can download and install it now. Although as usual you will be notified by MacVector’s online notifier in due course. 
We are pleased with this release and we hope you are too! Please feel free to let us know what you think!
Please note that this is a download only release and CDs will not be sent to existing customers.
I’m configuring access from the WordPress blog to cross post to the MacVector forums. So I thought it was a good opportunity to remind you about our forums. We have a fairly quiet but active community on our forums. They’ve been running since 2007 and there’s a lot of useful tips and topics on there.
As mentioned in the last few posts MacVector 11.1 is a release designed to consolidate and ‘tweak’ the many new features and changes that have been made over the last three years. In the main these changes are designed to simplify and speed up many common workflows as well as providing better integration with OS X and improving performance. However, there’s also some longstanding bugs that have been fixed and as usual a great deal of these changes have been made in direct response to users’ feedback. On that last point, as ever we encourage you to let us know what you think about MacVector, and whereas we always welcome emails to “support@macvector.com” and phone calls, we will be running a survey towards the end of this month to elicit feedback. The last survey we ran was quite a while ago now, and we got a some extremely valuable feedback. Incidentally we offered one of the new video iPods for one lucky winner last time, what cool new device from Apple could we offer this time…..!
We’ve mentioned a few of these changes over the last few posts, here’s an overview of the notable ones.
General
– Many of the analysis functions now use drop down window-modal sheets rather than application modal dialogs, allowing you to continue to work with other windows to prepare, view or copy data required for the analysis. Many of the sheets have a convenient new history combo box that keeps track of the various data files or target folders used in the dialog to allow rapid switching between commonly used files.
– Multiple levels of Undo have been added to the Trace, Multiple Sequence Alignment and Contig/Align to Reference editors. All three have also had extensive work to streamline workflows, add keyboard navigation and fix various display glitches and crash bugs.
– Dialogs to locate auxiliary data files (Restriction Enzymes, Matrices, Codon Bias tables etc) now all default to the appropriate location in the MacVector distribution folder.
– Align to Folder, Restriction Enzyme, Proteolytic Enzyme, Nucleic Acid Subsequence, Protein Subsequence, Translation and Reverse Translation are now all window modal dialog sheets.
– You can now drag a selection from one sequence window and drop it into another single sequence window or into an external application (e.g. TextEdit or Microsoft Word) that can accept drag and drop text.You can also drag selected text out of a result window and drop it into other acceptor windows e.g. Microsoft Word or Text Edit (OS X 10.5 and above only).
Subcloning
– You can now select any graphical object (e.g. a feature) and Edit | Copy will copy a blunt ended copy of the underlying sequence to the clipboard.
– The Ligation dialog now treats sequences copied from external sources or the sequence editor as blunt-ended fragments.
– Restriction/Proteolytic Enzyme – you can now specify the minimum number of cuts as well as the maximum number of cuts when filtering (or setting up) the results. The selected enzyme data file is now displayed in a history control so you can quickly swap between commonly used files.
Sequence Analysis
– Protein Analysis Toolbox – the AA Composition, pI and MW protocol now also displays the predicted extinction coefficients and aliphatic index. In addition, the pI and molecular weight calculations have been revised for increased accuracy.
– NA/AA Subsequence – the graphical Map result window is now linked back to the parent sequence so that selections in the result window are propagated to the parent editor.
– The Subsequence editor has been reworked as a dropdown dialog sheet and you can now copy/paste into the Sequence edit box. These changes let you easily paste primers from external applications or from other MacVector windows into a subsequence file to maintain a database of useful primers.
– There is a new “Show Dots” button that can optionally be added to the MSA editor toolbar (right-click on the toolbar and choose Customize Toolbar… to add the button). This represents matching residues in an alignment with dots rather than the residue itself.
– Growl installed on your machine, the Job Manager will use Growl notifications when a job has completed rather than bounce the icon in the dock.
– There are now keyboard shortcuts to switch between tabs – hold down the apple command key and type “1” to switch to the first tab, “2” for the second tab etc.
– “Dirty” windows now display a dot in the red window close button.
– Text windows and tabs now support standard keyboard and mouse selections.
The above list hardly scratches the surface of the full list of changes. You can check out the full list in the release notes.
MacVector 11.1 will be released in a few days.
MacVector 11.1 has had many changes that are designed to simplify and speed up many common workflows as well as to providing better integration with OS X and improving performance. A great deal of these changes have been made to improve the graphical Map view.
Performance
MacVector’s Map View allows the features and results (e.g. restriction enzyme sites) of a sequence to be graphically displayed. So displaying large AND feature rich sequences can result in a fairly slow Map. By large I’m talking about multi megabase sequences where there can be literally tens of thousands of features to show, all with individual labels and individual appearances. That can result in an extremely cluttered appearance. However, being able to visualise a sequence’s features becomes even more important as the size of the sequence increases. You can easily deal with the actual sequence and features of a single plasmid, but try that with a genome!
So to help with larger sequences the following enhancements have been made:
– For restriction enzymes the layout and performance (~20 fold faster!) of cut sites on crowded maps has been improved. Furthermore cut sites are now not displayed if the Map is so crowded that they would not individually resolve. You can view the hidden sites by zooming in to a smaller region or by right-clicking on the display and choosing “Show Results”.
– MacVector now automatically suppresses the display of feature labels for large sequences with many features (controllable from the Map View preferences pane). However, now when you hover the mouse over a feature, a tooltip displays the label of the feature. This is very useful for crowded maps or for when labels are switched off. Features are also now displayed on the inside region of circular maps to prevent features from overlapping each other or the sequence title.
– As well as increased performance the graphics view is now refreshed more optimally to reduce flickering and avoid multiple redraws of complicated layouts, for example when scrolling or resizing a window.
Label customisation
MacVector has always give the user great control in being able to customise the map’s appearance. By default the label of a feature will show the full description qualifier. However, the label can contain whatever you want. Obviously you do not want to waste lots of time changing multiple labels and so MacVector has metatags to define the information that is placed inside the Label. For example using the code below will show the name and location of a feature.
<Description> <Start> That’s really useful for restriction enzyme sites.
There are quite a few new metatags for MV 11.1.
<Size> displays the size of a feature in the label.
<Length> (functionally equivalent with the above metatag).
<Total> shows the count of this particular feature type
<Index> shows the order of an individual feature in the above number.
The last two above are also very useful for displaying restriction enzyme cut sites
e.g. <Desc> (<Index>/<Total>) would generate labels like BamHI (1/3)”, “BamHI (2/3) etc.
You can now correctly combine qualifier based metatags. That means <gene>(<number>)” will display My Gene (1) if the qualifiers /gene=”My Gene” and /number=”1” are present in the feature description. Qualifier based meta-tags are skipped if the qualifier doesn’t exist in the feature description (previously the actual meta-tag text e.g. <gene> would have been displayed).
Finally to make all this easier there is a new popup menu in the feature symbol editor that lets you view all of the available meta-tags and insert them into the label. Click on the small triangle to the left of the label edit box.
MacVector 11.1 will be released very shortly.
Technorati Tags:
MacVector
We’ve contemplated using Twitter in the past, but always hesitated to do so, as most ‘corporate’ users we see just use it as a pure marketing channel, and that’s quite boring! However, quite a few of us use Twitter personally and it’s a great channel to find out real information. With the release of MacVector 11.1 coming up we thought it was a good opportunity to use Twitter to notify users about the new release. So we’ve been quietly tweeting about the betas as they have been put up for download.
If you want to follow us, and we promise that it will be only be stuff that is interesting to a MacVector user….. here we are.
Technorati Tags:
MacVector
Over the next few weeks I’m going to be highlighting some of the new features that are being added to MacVector 11.1. The first of these is support for a great notification system that we all use at MacVector.
Some analyses with MacVector will take seconds and as such are done in the foreground. However, some types of analysis can take literally hours and if performed in the foreground they could tie up your Mac for a long time. MacVector has a tool called the Job Manager, whose sole purpose is to control such long running tasks. Once such a task is run MacVector will pass over control directly to the Job Manager, allowing the user to continue to use MacVector. As subsequent jobs are submitted it will store them in the job queue, only allowing them to run when there is a spare CPU (or core) to do so! Blast, alignments, primer design and sequence assembly are all examples of jobs that are submitted to the Job Manager.
Usually once a job has completed the Job Manager will notify the user using in the usual way by bouncing the MacVector icon in the Dock.
Growl is a third party open notification framework for OS X. It allows the basic notification system used by OS X (i.e. the bouncing icon!), to be replaced by a much more flexible, and potentially less intrusive system. It is widely supported by many OS X apps as a complete replacement for the OS X one.
We’re pleased to say that with MacVector 11.1 we’ve added support for Growl to the Job Manager.
Now whenever a job, that is running in the Job Manger completes it notifies you with a non-intrusive way. For example in the image above a Blast job has finished and Growl notifies you with the default theme, “Smoke”. If you click on the dialog then it will take you to the Job Manager where you can display the results. Otherwise it will quietly fade away. Although you’ll never forget you have results to view as the MacVector icon in the Dock will show the number of completed jobs available in the Job Manager!
MacVector 11.1 will be released very shortly.
So once again we find ourselves on a cold January day looking back at the year that has just been, and towards to the year that will be.
We’ve been very pleased that during 2009 we’ve had a record number of users contacting us with new ideas, and feedback on how MacVector works for them. Some of you had excellent ideas, and many of these ideas made it straight into the following release. For example accessing Vector NTI databases, Gateway cloning, displaying the 6 frame translations below the NA sequence in the editor and AutoAnnotation were all added in direct response to user requests made during 2009.
We’ve also been pleased with the releases we’ve made during 2009, especially MacVector 11. We’ve always aimed for MacVector to be the easiest sequence analysis application to use on the Mac. After all as we’ve said before the real work is made at the bench and in the thinking before that, not whilst sat in front of the computer. So the quicker you are able to design your experiments, then the more time you’ll have to write up those great results! With MacVector 11 Click Cloning became even easier to use and more powerful with the ability to manipulate overhanging ends and a new digest/ligate dialog in this release. This release also saw the introduction of Auto Annotation which is a great time saver for anybody who regularly has to curate their lab’s plasmids, or receives plain text sequences of cloning vectors.
2009 also saw the release of the fastest OS X version yet: Snow Leopard. We believe in supporting the latest version of OS X, and we made sure that MacVector 11 (which was released just before Snow Leopard) supported it straight out of the box! After all the January sales may see many of you with brand new Macs (well perhaps more likely to be from a successful grant application!).
Looking forward to this year we have MacVector 11.1 for release toward the end of this month. This release has a large number of changes designed to simplify and speed up many common workflows and to provide better integration with OS X. For example, there are now multiple levels of Undo for the Multiple Sequence Alignment, Contig/Align to Reference and Trace editor windows, and many analysis functions (restriction enzyme, subsequence searches, translation etc) now use drop-down dialog sheets. Other enhancements include the ability to import .ma4 files produced by Vector NTI, many tweaks to the graphics layout view (particularly for large sequences) and improved editing of Align to Reference and Contig Assemblies. In addition, there have been numerous bug fixes and underlying code cleanup so that MacVector 11.1 is more stable than ever.
Our biggest release during 2010 will be MacVector 11.5. This will be a click-cloning/vector construction release that will further improve the ease and functionality, as well as finally removing some long standing limitations. A long standing request is that you cannot currently select across the origin of a circular molecule. For cloning it means that you cannot replace a segment or easily create features that span the split point. That will be fixed and you’ll be able to rotate the molecule to any arbitrary split point. We also want to improve primer design to better support construct creation. The current Primer3 tool will be given a revamped interface to make it easier to use tailed primers and primers that have mismatches to the target. You’ll also be able to find restriction sites that can be changed into a site by a single base change. Allowing you to view only sites that do not modify any underlying open reading frames. There will also be continued work on the various graphic result windows to integrate them with the main Map tab. That will make it easier to convert results (e.g. open reading frames from the Nucleic Acid Toolbox) into features associated with a sequence.
Between these two main releases as we become aware of bugs or for example, any sequence format changes we’ll release minor updates as soon as possible to deal with these. As well as the big new functions we generally also try and add as many small bug fixes and enhancements as we can reasonably do into each release, all based on requests from users. If you have a new feature you’d like to see, or a pet hate you’d like to see fixed, please let us know and we’ll try and do something about it. We can also make minor changes that would make your workflows easier to both new and old functions, so make sure you keep that feedback coming in during 2010!
So here’s to 2010 and lots of success in whatever field you work in. We hope that MacVector will be able to help you.
Technorati Tags:
MacVector
Happy holidays to all users of MacVector (and everybody else!). We hope that 2009 has been a year of great experiments and positive result, and that MacVector has helped to make your life in the lab as productive and as easy as it could have been. Here’s to more success in your research, with astounding publications and happiness for all in 2010!
Here at MacVector we always try to listen to our end users when deciding what functionality to add to new versions. The more users that request a new feature, the more likely it is to get to the top of the list. One item that recently reached the top of our list was support for the Topo and Gateway cloning technologies from Invitrogen. MacVector 11.0.4 has a number of new additions that make it extremely easy to simulate Topo and Gateway cloning constructions with a few mouse clicks.
First, we added pseudo-Restriction Enzyme sites representing the TOPO and att recognition sequences to the Common Enzymes file. This is the file containing the default set of enzymes that are automatically displayed in the Map tab of all open sequences.
Second, we added a large number of Invitrogen vectors that are installed in the /Applications/MacVector 11/Common Vectors/Invitrogen/ folder. These include a selection of “Entry” and “Destination” vectors. Others can be downloaded from the Invitrogen web site – you can use MacVector’s Auto-Annotation function to quickly annotate additional vectors with common TOPO and Gateway features.
A typical Gateway cloning vector with att and TOPO sites highlighted.
Its then very easy to simulate a TOPO or Gateway cloning experiment to create a constructed molecule with the identical sequence at the junctions to the one you would get in the lab. To clone a PCR fragment, simply select the region in a source molecule (or from an external text editor) and copy it to the clipboard, then select the TopoTA/BLNT site in the vector and click on the Ligate button. A Ligation dialog opens showing you the compatible blunt ends.
This gives you the option of flipping the source fragment if you wish. Note that this also works for TA cloning as well as ZERO-BLUNT cloning manipulations, even though the dialog does not show the overhanging T-A ends.
When Ligate is clicked, the fragment gets inserted into the vector. To perform a Gateway cloning, you can select the two att sites (attL1 and attL2) and copy the fragment to the clipboard.
Then open a suitable target/destination vector – these typically have attR1 and attR2 sites.
Now when you click on the Ligate button you’ll see the core recombination sequences of the att sites shown as overhanging ends.
Note that there is a single residue difference between the core sequences of the attL1/attR1 and attL2/attR2 sites;
The single T-C mismatch between the two core sequences ensures that the att recombination can only occur in one orientation. MacVector understands this and will automatically flip the source fragment if needed so that it becomes inserted in the biologically correct orientation. Finally, clicking Ligate inserts the fragment into the target vector.
For a more in-depth discussion of the new Gateway and TOPO cloning functionality in MacVector, download the Gateway and TOPO Cloning Tutorial from our web site.
One of the great things about OS X is that updates are really painless to install! Actually come to mention it upgrading the OS between major versions is usually trouble free too! For minor in version updates System Update will easily download and update the OS, leaving you the user to just reboot. So really there’s no excuse to run an older version of an OS! Of course as well as being painless OS updates generally include many important bugs found by Apple.
An good example of one of these bugs is a recurring one we’ve found with early versions of OS X 10.4 (Tiger). We’ve had many users report this one. The bug in the operating system causes MacVector to crash when loading the “online update” message from our website. Quite annoying and not our fault we assure you! Updating to 10.4.11 (the last update of this OS) solves the problem.
A more current example is a bug that we have just found in the search function of the file open dialogue. If you regularly use this to open files, and you have recently upgraded to Snow Leopard, then it is likely that you will start experiencing some hangs. Unfortunately once again the bug appears with OS X and not with MacVector, so there’s not a lot we can do! We’ve reported the bug to Apple. In the meantime we recommend using a different way to open your files until the bug is fixed!