Thanks for trying BioAssistant! We hope you find it to be useful in your everyday PCR chemistry applications, such as probe setup and design, MasterMix solution protocol setup, DNA sequence manipulation, and Peptide visualization.
BioAssistant is based on Chaotic Software's first PCR chemistry applcation, Probe Assistant, but takes it a huge step forward by introducing a whole lot of new features, redesigned interface, and a bunch more. Feedback, as usual, is very welcome at Chaotic Software. In this case, though, applications of this nature must be accurate, and based very much on what YOU, the chemistry (or other life science discipline) lab user, would like to see in such a software package. Therefore, if you find any bugs, or if you have some suggestions for improvement, please let us know.
II. Quickstart
To use BioAssistant, there is not much to it—just double-click the application and you're ready to go! If you have not registered with Chaotic Software, an opportunity to purchase will appear each time you start the application on the splash screen. To dispose of this dialog, enter the registration code sent you by Chaotic Software. If you do not have a registration code, follow the steps in the next section ( "Registration" ) on how to obtain one.
III. Registration
To register, simply run the application, and at the splash screen, click the "Buy Now" button, which will take you to the purchase web site for this product. Fill out the information, and you will be e-mailed a registration code for entry in the splash screen dialog. All transactions are 100% secure via the on-line store.
IV. Using BioAssistant
BioAssistant is document based; users should open a new worksheet by selecting "New worksheet" from the file menu, edit their PCR probe setup, and save it just as they would in a word processor.
As you can see from the above picture, worksheets consist of a series of tabs, each pertaining to different pieces of the overall PCR probe setup. Above, you can see the "Solution" tab, which is the default tab of any new worksheet. At the top of each worksheet is an editfield for the Probe's DNA nucleotide sequence, which can consist of A,C,G,T,R,Y,S,M,K,W and N.
Worksheet Tabs
Solution ...... On this Tab of the worksheet document, users can enter the parameters of their PCR solution, including ingredient concentrations, "Dangling Ends", etc. If you have any ideas on what else you would like to see on this tab, or how these factors should affect Analysis, please e-mail the developer directly at jgiles@chaoticsoftware.com.
Rxn/Abs ...... This part of the worksheet contains settings for selection the Reaction Type and Absorbance parameters. Currently users can only determine absorbance based on the A260 and Dilution Factor values, not wavelength.
Markers ...... Here the user can set what types of Markers the pcr probe has attached, if any. These may be TaqMan (™Roche Molecular Systems) flourescent-dye markers, or the users own custom markers (all values must be provided by the user in this case). Also in this tab is an option to exclude dyes from analysis, even if you have entered Probe Information.
Analysis ...... This tab panel shows the analyzed values of the nucleotide sequence as specified in the Sequence editfield. It is a calculation based on values set by the user on the Solution, Rxn/Abs, and Markers tab panels. There are two sections to the Analyzed values, "Temperature" and "Physical Characteristics", which help the user design a probe appropriate to the chemistry system they are attempting to use.
Coefficients ...... This pane shows the calculated molar extinction coefficients of the DNA by itself, as well the DNA with probes attached. Obviously, if the user has not entered probe information, these values will be the same.
Comments ...... Finally, this tab is used for user's personal information, where you can enter a name for the primer, dates of creation and modification, as well as miscellaneous comments.
Analyzing Your Sequence
Once you have entered in the proper parameters that describe your primer, you can analyze those parameters by using the CMD-K keystroke, or by selecting "Analyze Primer" from the Primer menu. It should be almost instantaneous, and your calculated values should appear in the "Analysis" and "Coefficients" tabs of the worksheet. See "Analysis Options" below on how you can modify the parameters of the analysis.
V. The Tools Menu
Sequence Converter
Users can use this tool to manipulate nucleotide sequences. Putting a sequence in the "Original" edit field and clicking the convert button yields the sequence's compliment and reverse. This is extremely handy if you are in need of a long sequence in a different configuration for your experiment. There are also two different options in this dialog for the conversion, including one that will strip out invalid nucleotide characters and another that will make the resultant compliment sequence an RNA strand.
Amino Analyzer
This tool provides the user with a visual representation of a nucleotide sequence in terms of individual peptides, dividing the sequence into 3 letter codons pieces and then showing the result graphically. This tool also will output the length of the provided sequence, and total number of three letter codons. Optionally, the user can change the conversion into a one letter view consisting of the amino acid abbreviations, and users can also change the colors of the resultant graphical view.
Master Mix Calculator
Finally, the Master Mix Calculator allows the user to enter in values for their PCR master mix solution, and print out a summary of the resultant solution. Parameters include stock concentrations and their volumes, as well as number of desired reactions, single reaction volume, and a percent pipetting excess. There are several pre-defined PCR protocol setups in a pop-up menu, where the user can select a protocal that closest fits their desired PCR reaction solution. You can also save a MasterMix setup by using the "Save" and "Delete" buttons. Simply enter a unique name for your setup in the "Name" textfield, and click the save button. You new setup will appear in the Protocol menu, and whenever you want to reload that setup, select it from the pop-up. If you want to change a setup, simply click the "save" button again while the protocol of choice is open. If you would like to discard a setup, make it active, then click the "delete" button.
VI. Analysis Options
There are several options that affect the way BioAsstant performs it's calculations on the user's nucleotide sequence. The main parameters are those that appear in the worksheet tab panes, but others appear in the Analysis Options dialog, which can be accessed by typing Command-T, or by selecting the "Analysis Options..." from the "Primer" menu.
Processing Options
These options affect the analyzed values on the worksheet.
The first checkbox Remove Invalid Letters from Sequence, removes any invalid nucleotides from the user's current sequence. Valid nucleotides are: A,C,G,T,K,M,S,R,L,W and N.
Beep When Analysis Is Complete determines whether or not BioAssistant beeps after analysis. The analysis is so fast however, there isn't much need for this... ;-)
The last option, Tm Calculation Method, is a popup menu that affects the way the the melting temperature (Tm) is calculated. Currently BioAssistant has two methods of calculation: the "Wetmer" method, which is the same calculation performed by Probe Assistant 1.0, and the "Standard" method which calculates the melting Point a bit differently. If you wish to see the formulas used in calculating the Tm, use the "Verbose Logging" feature discussed below.
Log
The Generate Log During Analysis, causes an "Analysis Log" window to open with a breakdown of all steps that occur "under the hood" of BioAssistant. This allows the user to have a window into the heart of the application's analysis, so they can see how they got their analyzed values.
If the user activates the Use Verbose Logging checkbox, the log output expands to include formulas used in the intermediary steps and the values obtained in those steps. This way the user can see a blow-by-blow account of the analysis, and how their values were calculated.
Finally, the Clear Log at Start of Each Analysis checkbox determines whether or not the log window is continually cleared on a new analysis. If it is not checked, the new analysis will be added on to the end of the last analysis, until 32K of text has been put into the window, at which point it will be truncated.
NOTE: The Log window information is NOT PERSISTENT. Closing the "Analysis Log" Window causes all Analysis info to be LOST! If you want to save this information, you should copy and paste it into another application.
VII. Preferences
The Preferences dialog can be accessed by either selecting its menu item from the Edit menu, or by pressing CMD-G. There are several application wide preferences here, where you can tailor BioAssistant's behavior to your specific needs.
General: These are preferences related to General BioAssistant functionality as well as the Tools found in the "Tools" menu.
- The Speak Sequence As It Is Typed enables BioAssistant to speak A,C,G,etc. as they are typed into the Sequence Editfield in a worksheet. This is mainly for error-correction as you type in the sequence.
- Default Master Mix Protocol affects the "Master Mix Calculator" tool; the menu item chosen here affects which type of setup you wish to come up as the default when this tool is opened.
- Open This Tool On Startup is a great option if you plan on using BioAssistant's tools most often. Selecting one of the menu items causes that tool to pop open each time BioAssistant is opened.
Primer Worksheets: These are preferences are related to working the Primer Worksheets and thus only affect this area of the application.
- Open a New Primer Worksheet on Startup causes a new primer worksheet to open each time BIoAssistant is started.
- Default Sequence for new worksheets allows you to enter a starting sequence that will be put in every new Primer Worksheet that is created.
- Save Worksheet Changes Automatically updates your file with any changes you may have made to the opened worksheet without asking. This is a great for dismissing that pesky "Save/Don't Save" dialog (this problem will be alleviated in future revisions), but can be dangerous if you want to discard any changes you may have made to your document. Set Tips and Troubleshooting below for some pointers on using this feature.
- Use Name for Summaries is a feature that is no currently used.
- Default Reaction Type allows you to pick the type of reaction you use most commonly. This reaction type will be used in any new worksheet you create.
Clicking OK will save any changes you make to the preferences and dismiss the dialog. Cancel will discard any changes you have made.
VIII. Tips, Troubleshooting, and Known Limitations
Tips and Troubleshooting
Printing: Printing in BioAssistant is fairly rudimentary, and will not provide you with much feedback or options. Most windows are printable, including the "Analysis" Log windows, etc. If you are not printing properly, we recommend that you attempt to print this document. If this fails, the problem is not BioAssistant, but some other OS problem; perhaps there is not printer selected in the chooser, or your printing queue is turned off. Check these problems and then try again.
Saving Files: File saving in BioAssistant 1.0 is a bit rudimentary. It is not smart enough to know if you have saved your changes previously or not, and therefore it will ask you each time you attempt to close a document if you would like to save your changes. If this is bothersome, there is an option in the "Preferences" dialog to "Save Changes Without Asking", where you can simply save any changes made to your document automatically when they are closed. Be forewarned, however, that it WILL save ANY change made, and if you do not want these changes made, you must disable this option temporarily to discard changes.
That pesky registration dialog keep coming up!: To get rid of the dialog that appear on startup, you must register the application with Kagi. See the "Registration" section of this document on payment instructions.
I click the "Register" button, but it just beeps at me!: This is most likely because you have not entered the proper registration code in the "Registration Code" text area. Be sure you carefully enter the registration code exactly as it was given to you by Chaotic Software. If you have sent your payment to Kagi shareware, but have not received your code, please send us e-mail and we will send you a code immediately. Send code requests to: jgiles@chaoticsoftware.com.
TIP: You can navigate up and down through a worksheet's tabs by using the CMD-UP ARROW/CMD-RIGHT ARROW and CMD-DOWN ARROW/CMD-LEFT ARROW key combinations. This way your fingers don't have to leave the keyboard.
Known Limitations
Printing: printing is extremely rudimentary is this version, with capabilities for only printing certain windows, etc. There is also no real "report" generating features. Summaries are the only outputs currently, and these are not implemented in all dialogs.
Saving: this is probably the worst offender of the group— there is no smart method of keeping track of changes, and thus you are constantly prompted when closing worksheets. See above for suggested workarounds.
Summaries and Logs: When a summary window first is opened, it's contents could be cut off the bottom, and the scrollbar is not active, thus you cannot scroll down to see the end of the summary output. Simply resize the window and the scrollbar will become active.
Note about Known Limitations: If you feel this is a useful product, please let us know! Most, if not all, of these limitations will be addressed in a future version, but only if feedback is received! Thus, please feel free to e-mail with any suggestions, criticisms and/or general feedback, to: jgiles@chaoticsoftware.com.
IX. FAQ
This section hopefully answers all common questions.
What is the general shareware information?
BioAssistant is shareware, which means if you like it and continue to use it, you should pay for it.
The cost is $20 for a single-user license, $200 for a site license (unlimited use at a single site), and $500 for a world-wide site license (unlimited use at as many sites as you need). All prices and options are shown in the Register application. Please use the Register application to ensure proper registration with us, and also so that we can provide you with any needed support.
Can I distribute BioAssistant?
Yes, please do! You may distribute this application anyway you want as long as you include the documentation and Register application and do not charge for it. (Reasonable media and distribution costs excluded.) We want as many people to get this product as possible.
What did you use to create BioAssistant?
BioAssistant was written in C/C++ using Metrowerks CodeWarrior and PowerPlant. Resources were created and edited with Resorcerer 1.2.5.
Do you have anyone to thank?
• Kagi Shareware for providing an excellent service for shareware authors.
• Thanks to all the people who have registered!
X. About Chaotic Software
What is Chaotic Software all about?
We (Bob Bradley and Jason Giles) had many software ideas we wanted to release to a wider audience for test and use, and decided a company was the best way to go about it. So we formed this partnership that will, from time to time, produce new software products that we want on our Macs. Our main purpose is not to reinvent the wheel, but present solutions in certain areas of the software industry that we feel are either beleagured by featuritis, or have poor or no implemenations available for the Macintosh.
What other applications have been released by Chaotic Software?
FlavorSavers • The ultimate Macintosh screensaver. $24.95
MacArmyKnife • The swiss army knife of Macintosh utilities. $24.95
MP3 Rage • The ultimate MP3 toolset, featuring a Napster client! $24.95
Web Devil • Suck down web sites without the need of a browser! $34.95 Shareware.
AutoTextTyper • Types frequently used text with a hot key or contextual menu click. $10 Shareware.
BioAssistant • A tool for PCR chemists who develop DNA probe sequences. $20 Shareware.
Drop•Attribute • Fast and simple Type/Creator/Attribute Changer. $10 Shareware
Drop•Rename • A powerful file renaming tool. $10 Shareware.
Manipulator • The ultimate file manipulation utility. $20 Shareware.
Nag • A flexible personal scheduling application. $10 Shareware.
NetClip • Share clipboards over an intranet or the Internet. $20 Shareware.
Probe Assistant • A tool for PCR chemists who develop DNA probe sequences. $10 Shareware.
QuickMovie • Make QuickTime movies out of a series of images. $10 Shareware.
Web Timer • Suck down a single URL repeatedly! Great for webcam monitoring. $15 Shareware.
Web Watcher • Watches your favorite web sites and notifies you when they change. $20 Shareware.
Do you have any Web Pages?
Of course! What savvy company does not have a page these days? Please check out our site for new product introductions, product information, and software updates. The address is:
http://www.chaoticsoftware.com/
Where can I contact you?
If you like this program or if you even think it sucks, let us know. We always answer our mail so, if you don't get a response, we may not have received it and you should send it again.
For help or general information about this application and/or Chaotic Software, Ltd., send mail to chaotic@kagi.com.
For information about Kagi Shareware and/or the Register application, send mail to shareware@kagi.com.
To contact the author directly, mail Jason Giles at jgiles@chaoticsoftware.com.
