I've started a YouTube channel with tutorial videos. There are 11 so far in the tutorial playlist. Let me know if you have requests for any topics I should add to the tutorials.

Just posted the 3.1.8 update. Let me know if you find any bugs. It opens in inline feature mode. If you prefer compact mode or if you are opening large sequence files, you can turn off inline mode in Preferences (aka Settings).

RT @ATinyGreenCell: Here's a tutorial I wrote on how I design detection and cloning primers using Primer3. Hopefully it's helpful for stude….

The one I use most is the molar reaction calculator- DNA assembly reactions can be more efficient if you have a consistent molar ratio of input fragments. If you have the size of the fragment and your concentrations, you can calculate the volumes of each DNA solution required

You can store reactions that you use a lot and multiply a master mix recipe

It also has a simple c1v1 c2v2 calculation

You can calculate the weight of an average DNA, or a specific DNA sequence

If you have a recipe that looks like:.100mM CaCl2.1M NaCl.50 mM glucose.you can copy that text, set your desired volume (ex. 1L), press the calculate button, then if you do a paste back into your text editor, you'll get:.100mM CaCl2 11g.1M NaCl 58g.50 mM glucose 9g.

from this, you can calculate concentrations

Here's my first attempt at a web pages documentation. This one is for the Golden Gate Assembler tool. Let me know what you think.

I've uploaded new versions of ApE 3.1.7. The Mac version didn't have the correct version number in the "Get Info" window. The Windows and Linux versions had a small bug that prevented them from running. All three errors should now be fixed.

I just uploaded version 3.1.7. This update fixes a bug that caused failure to recognize some substrates in the Recombination reaction tool. Also the first full version with the option of inline feature display (option in the preferences).

New bug fixes for theme save, Molecular reaction calculator.

New bug fixes, including BBEdit fix. Also a Linux version.

I'll post any new bug fixes as later replies to this thread.

Win: mac: you have to go into settings/ preferences and select inline mode (and selection highlight on top) to use the inline mode.

I'm updating the user interface of ApE. Features and enzyme sites are inline with the sequence. If you can give it a try and email me all the bugs you find, that will help me get this out into wide release.

I also fixed the "PIN number" problem in the PCR menu item.

As always, let me know if you have any problems or find any bugs. I'm also curious for feedback on the circular map themes. If those are working well, I'll implement them on the linear map too.

I just posted ApE version 3.1.6 to the website. This fixes bugs in the recombination assembler, PCR eaction tool, and keyboard shortcut keys on the Mac.

Feedback is super valuable to the development of ApE. I've got the demo theme files up on the website. If you try them out, let me know if you have any trouble or suggestions for improvement.