Programmation

AmplifX Version History

Nov. 21 2013 : version 1.7.0

- The Mac version is now a Cocoa application (compatible Mac OS 10.9 Mavericks and Retina displays)
- Very big sequences support (> 1 million nucleotides)
- Huge improvment in speed for almost all time consuming operations : sequence and primer list loading, match searches, primer design, ... (Thanks to help from Theodore H. Smith. This guy is a genius !)
- The program is now distributed as a multilingual bundle (still only in english and french but translators are welcome)
- Multi-criteria sorting of primer list (see the new menu "primers > Sort using multiple criteria...")
- Ability to change the primer order in the list by drag and drop
- New interface element (slider) in the main window that allow to quickly change the required number of perfect matching 3’end nucleotides in the match search alogorithm (without going to the Preference window)
- The menu "paste complement strand" now works into the field "use this primer" in the primer design window.
- Behavior improvment of the menu "Undo"
- Graphic view zooming improvment
- And a lot of bug fixes and algorithm corrections !

Feb. 5 2013 : version 1.6.2

-IMPORTANT : fix a serious bug in version 1.6.1 that can corrupt primer list IF AND ONLY IF one saves primer list AFTER sorting it and add new primers since yet. IF it’s the case, please contact me with the feedback form so I can help you to repair your primer list !
- Improve : after reseting the preferences, the default column widths are restored
- Improve automatic ID proposal for new primers

Jan. 10 2013 : version 1.6.1

- [Win] fix : primer lists shared by SMB work
- Fix : no more crash when opening primer lists saved by AmplifX prior to 1.5.0
- Improve : Alert box

Dec. 15 2012 : version 1.6.0

- New features :

  • Linux version (32bits - GNOME). Tested on Fedora 17 and Ubuntu 12.04 with GNOME-classic (not compatible with Unity !).
  • Filtering system of the primer list : as you type on the classic search field, the primer list is filtered instantaneously ! Possibility is given to restrict to the matching primers.
  • New column in the primer list : a color code that is associated to category or family (or anything one needs). The colors are used in the graphic map to figure out the corresponding matches. -*Possibility to limit the size of the amplicons (default=3000 bp) (see the text field near the "run PCR" button.
  • Primers can match even if they exceed the target sequence (limit is 254 nucl.)
  • New menu : "invert case". Specially useful with the new primer design options (see above)
  • Windows version is distributed with a Setup (thanks to Inno Setup)
  • Mac version is distributed on a disk image (.dmg)
  • New menu : "Window"
  • New menu "New primer list"
  • A click in a “match” automatically selects the primer on the list. But the active tab remain the same (previously it systematically showed the info’s panel)
  • Primer design : add the criteria "GC clamp" to design primers ending with a chosen number of (G,C).
  • rimer design : new search option for primers ending with N nucl matching on part of the target sequence typed as lowercase. It can be of special interest to design specific primers on a mutant for example.
  • Primer design : the special options are hidden to not overload the interface
  • Primer design : No more upper size limit for the amplicon size
  • The match information (info tab) displays the start and end position on the target.
  • Primer list : if the ID is found in duplicate, an alert (duplicate ID) is added after it.
  • Application launching : if the program try to mount a network volume : a window tells the user to be patient. The timeout is managed by the operating system and not by AmplifX.
  • Graphic map : as the mouse is over a match, the corresponding amplicons are automatically sorted on the top of the map.
  • Application launching : if a new version is available a message is shown.
    - Primer list : one can now choose which columns one want to export and the order.
  • Degenerated primers : a new option (in the preferences window) tell the program to not try to match primers too much degenerated (default : 256) (the degenerated sequence ACGTSN means A, C, G, T, (C or G), (A or C or G or T) and the fold of degeneracy is 1x1x1x1x2x4=8
  • One can add multple pairs of primer from the design Window to the primer list
  • A new dialog while importing primers allows the user to tell which columns and which order they are in the source file.
  • [Mac] Target sequences can now be open by drag and drop onto the dock icon.
  • Drag-n-drop anywhere on the main window allows to open primer list and target sequences
  • A splitter separate the window in height to customise the respective height of the upper elements (primer list and all the stuf in the tab viewer) and the graphic map above. (It prefigures some new features coming soon !)

- Improvements :

  • "Run PCR" button behavior enabling/disabling improved.
  • Primer list contextual menu improved
  • Graphic map zoom improved
  • Menu "paste complementary strand"
  • The locking system used to avoid overwritten by an other user uses an invisible file which a name beginning with a ’.’. These names are not allowed on every system so AmplifX uses now an alternative name with ’__’ at the beginning.
  • Primer list edition improved (very annoying bugs in Windows are now corrected) Search function improved, the "search on lower strand" functions.
  • Mac OS : Command H is used as waited for hide AmplifX and not to show the help.
  • Mac OS : Dramatic improvement in trimming a pasted sequence.
  • Primer design : the "search" button is disabled after a search until the criteria or the sequence are changed (to avoid clicking by mistake and wait again !)
  • No more alert message with big target sequence (the program can manage very big sequences depending on the performance of your PC/Mac)
  • Primer design : coherence between each search criteria is improved
  • Corrections and coherence in the numbering of the size and base position of matches (always the 5’ of the primer and not the 5’ of the match in the target sequence)
  • Primer design : Correction of the difference of one in the criteria fields and the return values of the found primers.
  • Bug correction of the deletion of one nucleotide after "redefining the origin"
  • Windows : zoom animation improved.
  • Improve : primer list editing
  • Improve : behavior with big target sequences
  • Improve : speed in primer list loading

Oct. 28 2008 : Version 1.5.4

- Minor correction of version 1.5.3 : calculation of amplicon size was distorded by previous correction of reverse primer position (thanks one more time to Savio, the current champion in bug detection !)

Oct. 20 2008 : Version 1.5.3

- Cosmetic : suppression of text overlapping in some alert dialogs
- New option “exclude lowercases” in the primer design’s window (yet implemented in version 1.5.2 but not explained !). This option allows for example to find primers that don’t match against lowercase typed nucleotides in the target sequence. It’s especially useful, for example, to make specific primers for one sequence in a family (type non conserved bases in uppercases) or in the contrary for primers matching conserved regions (type conserved nucleotides in uppercases).
- Redefining the target sequence origin can now be done by a right-click onto the target sequence after inserting the cursor at the desired position.
- Primer design : correction of the calculation of the reverse primer position in the result’s list (bug reported by C. Savio Chan)
- Primer design : adding information to the primers when added to the current primer list : target name, matching position, design date, …) (Feature asked by C. Savio Chan.)
- Preference window : correction of min and max cutoff scores for weak and strong matches. Sorry this bug appeared in the previous version because of an anticipation of a next major rewriting of the virtual PCR algorithm. (Thanks one more time to C. Savio Chan to saw it.)
- Search function : correction of some bugs in the “search all occurrences” option.

Sept. 15 2008 : Version 1.5.2

- Normal behavior of esc key when the cursor is in a cell of the primer list : the cell simply looses the focus and no spaces are typed. (Thanks to Lars Henning to have reported this bug.)
- Correction of the GeneBank importation : a G was systematically added at the beginning.
- Possibility to directly import ApE file formats (GenBank format in fact with special file name extension.)
- Correction of a crashing bug when importing target sequences with some special Unicode characters (thanks to Damien Hermand to report this bug.)
- Keeping registration key when restoring pref files with default values. (Sorry for guys that needed to register AmplifX again !)

Jul. 10 2008 : Version 1.5.0

- Modification of primer list format (automatically updated when open with AmplifX 1.5.0 or superior).
- To work on a shared primer collection into a team or a lab, the best way is to use the same primer list file into the local network. To help working in this way, now, AmplifX manages a locking system that allow only the first user to write into the primer list and save changes. The other users can only read the file and must « save as... » if they make some changes. After the first user close the file, the lock is destroyed and one other user can reload the modified primer list and make its own changes.
- A new column « Owner » is especially useful in the context of shared primer list. Its entry is made easier by a scrolling menu.
- Heights and widths of the columns of the primer list and size and position of the main window are restored at each launching of AmplifX.
- To each new added primer, an id is automatically created (it can be changed by hand, of course). The program analyses previous ids and increment them : they can be constructed with any prefix and a number possibly formatted with a constant number of digits : example Pr0001, Pr0002,...
- End of line characters are forbidden into any primer list fields : Enter and Return keys are managed in the same way as the tab key : editing of the next field.
- Add amplicon size information into found primer pairs of the Primer design window.
- The primer design window is not resizable anymore.
- Management of expiration date for the beta releases of AmplifX -Drag and drop is now properly managed into the target sequence text field : dragging from an outside source (text editor, web page) insert recognized ATGC (upper and lower cases) at the insertion point. But dragging from the target sequence field itself is forbidden. Because it has appeared to be triggered accidentally (while playing with selection for example).
- Automatic fetch for AmplifX updates.
- Automatic request for registration (after using AmplifX for a while) by an integrated form. (Note : registering and giving some feedback is not very time consuming but very motivating and interesting for the kind developer that improve this program in his free time.)
- Fixing paste function in the search dialog and in the ID and description of the primer list.
- Fixing zoom function triggered by the drag + cap key : the zoomed map is well centered on the dragged region.

Sept. 25 2007 : Version 1.4.4

- Correction of a bug attached to the release 1.4.3 : in the primer sequence, when one wanted to paste or copy with keyboard shortcuts (Apple+V or C in Mac or Control+V or C in PC world) the appropriate menus were applied but with a prolonged pressure on the two keys : the system passed the second one and the program interpreted it as a base (C for Cytosine or V for « not U » in the IUPAC nomenclature i.e. A or C or G). Thank you very much to Patrick Trieu Cuot who reported this annoying bug. (and thank you for citing AmplifX in his last paper).

Sept. 19 2007 : Version1.4.3

- [mac] The Mac version is now available as Universal Binary (3x faster onto Mac Intel).
- New interface : the primer’s additionnal informations are at the right of the primer list in the same window : the previous drawer window behaved strangely and the comment field was under used.
- One can now simply select a region into the target sequence and tell AmplifX to design primers to amplify it (Thanks to David Cittaro for this suggestion).
- A double click into the target sequence selects the block with the same case (lower or uper). It’s specialy useful with the previous point.
- Delete key does its job in a primer sequence in the primer list.
- Tab key works to edit the next cell in primer listt.
- One can search into the complement strand in the search dialog
- [win]The Windows XP Interface is less weird ( !) : I have understood what’s the MDI and gave it up (but it’s still far as nice as the Mac version !).
- Limit the scale of the graphic map to avoid losing it when one Maj-clicks without draging
- Save as menu gives a new name with « copy » at the right place (before the extension).
- Correction of the Primer list columns helptags.
- Correction of a bug when importing an AmplifX primer list
- TM and qualty is limited to primers shorter than 100 bp to avoid to kill your computer.
- Comments are not lost when one changes the sequence of a primer.

Oct. 4 2006 : Version 1.4

- AmplifX is now written and compiled with RealBasic 2006 : that make it a "true" Mac OS X application (for the Mac version of course !)
- It supports now degenerate primers : a long awaited feature by many of its users.
- It can export its graphic maps in vectorial formats

  1. PICT : an historical one and still used in numerous applications like the Crimosoft suite.
  2. SVG a new and very beautiful format too less used. (have a look at http://www.svg.org for general informations about SVG and http://www.inkscape.org for a free SVG editor. (You will never use Powerpoint anymore to make your posters !)
    - it corrects somme bugs (translations, help tags,...)

Nov. 11 2005 : version 1.37

(Special thanks to Lars Henning and Sam Lukowski for theirs feedbacks)

- AmplifX is now written and compiled with RealBasic 2005. This allows to fix some bugs due to the « old » RealBasic version ; specially some very constraining bugs in the Windows version. (Thanks to Lars Henning for his very useful feedback.)
- New icons.
- Improvement of clipboard linked menus and « Undo » menu.
- Improvement of appearance and behavior of the drawer window giving more information about primers. This window is now only shown and masked with a single button located in the upper right corner of the primer list box. The drawer appears only in the right of the main window and if needed the main window resizes or moves itself.
- Improvement of menu activations.
- Add (partial) Contextual menus management.
- Add new help tags and new menu to activate/deactivate « contextual help »
- Change the mouse position indicator onto the sequence map. It’s more esthetic and more functional. (And fix zoomed map positions)
- Mac OS X : Dot close button management linked to the primer list modifications
- Preference window is now viewed as modal window and can be displayed from the Design primer window.
- Add the possibility to visualize more than 10 best scoring primer pairs in the design window. (1 to 1000). (The new algorithm is a little bit less efficient for sorting the 10 best pairs but much more efficient to sort the 1000 best pairs.)
- Improvement of the application quitting process while the design primer window is visible.
- New calculation for the suggested annealing temperature after Chavali,S. et al. in Bioinformatics 21 pp 3918-3925 (2005) (With Amplicon TM calculated with the NN method).

Sept. 6 2005 : Version 1.31

AmplifX 1.31 corrects some bugs :

Clipbord management with paste and paste complement strand in the Primer List

Unwanted trimming of characters different from ATCG into ID and descriptive name (Thanks to Ralf Kölling who have report this bug)

Non drawing of very short amplicons, even after zooming in.

Sept. 2 2005 : Version 1.3.0

- New “Undo” menu : to cancel the last modification in the target sequence field and in the primer list.
- New algorithm and coding of the mapping and drawing of upper/lower cases. (More than 10 times faster).
- New graphic element : the current selection in the target sequence is visualized by a semi transparent blue region over the sequence map line.
- Color code for upper and lower regions are now fixed : In the previous releases it was always the same first color in the map whatever the case.
- New colors in the graphic elements (I expect a little bit less ugly !)
- Benchmark tests : I determined the maximum size of the target sequence beyond which AmplifX slows too dramatically or even crash. That depends mainly on the system. The Mac version begins to have problems beyond a few tens of thousands nucleotides. The Windows version works better (!) and support a few hundred of thousands nucleotides. A message warns the user when the sequence exceeds an arbitrary limit for each platform : 70 000 for Mac and 300 000 for Windows.

Jul. 26 2005 : Version 1.11

- Correction of a shift in export and impression views.
- Left and right arrows are now used for navigation into one cell of the primer list instead of navigation through neighbor cells.
- New function : « Export checked primers ’ : create a tab delimited file containing sequences and ids of checked primers. It can be useful, for example, to quick order new designed primers.
- Search into the primer list is able to search in the comment field. (The Comment Field is visible when the drawer window is open. Remember that you can use it to put everything you need as additional data like target sequence, boxes and freezers, etc.)
- Correction of a bug linked to the use of the return character into the comment field.
- Change menu « Free Registration » to « Send feedback » to encourage users to share their ideas.

Feb. 7 2005 : Version 1.11

Once more thank you to Patrick Trieu-Cuot for his suggestions and encouragements.

New features :
- New function of primer design : AmplifX searches for pairs of primers with no, or one or the other of both primers fixed. (Algorithm in the course of improvement, welcome experience feedback) - Print and export of the chart.
- Support of DNA Strider files as target sequence (of which a new version for Mac OS X is available)
- New information on the amplified sequence : addition of a suggested annealing temperature for the PCR. (According to Rychlik.W et al. in NAR (1990), vol. 18 pp 6409-6412)
- Possibility of searching sub-sequences in the target sequence (access by the menus already existing employees yet for search in the primer list)
- Use of styled text for the copied amplified sequence : useful to quickly locate the primers, when the sequence is pasted in an application which support styles

Corrections and improvements
- Adequacy of the use of the relation "Superior or equal to the cut off" for the drawing and the search for matches
- the use of right and left arrows, and the suppress key work in the « numeric-range » fields of the preferences’s window
- Correction of an error occuring while importing GeneBank format files.
- Correction of the display of information of the current selection of the sequence target at the time of the use of the menu "SelectAll", "lowercases", "uppercases" and while un-selecting
- Maintenance of the lower/uppercases features on the complementary strands
- Best updating of the “ default file “ radio-button state after a “ save as “ operation.
- When the window of search is displayed, the focus one is put into the field of search to avoid typing into the target sequence.
- Correction of a bug related to the list of the recent files preserved in the preference file and which could involve in certain circumstances a crash at AmplifX starting and whose only solution was yet to delete the preference file. - Correction of a bug that could occur if the quality scores had to be re-computed at the automatic loading of the primer’s default file.
- Correction of the placement of reverse primers over the chart (for small amplified fragments the primer length is not negligeable)

Feb. 7 2005 : Version 1.1

Once more thank you to Patrick Trieu-Cuot for his suggestions and encouragements.

New features :
- New function of primer design : AmplifX searches for pairs of primers with no, or one or the other of both primers fixed. (Algorithm in the course of improvement, welcome experience feedback) - Print and export of the chart.
- Support of DNA Strider files as target sequence (of which a new version for Mac OS X is available)
- New information on the amplified sequence : addition of a suggested annealing temperature for the PCR. (According to Rychlik.W et al. in NAR (1990), vol. 18 pp 6409-6412)
- Possibility of searching sub-sequences in the target sequence (access by the menus already existing employees yet for search in the primer list)
- Use of styled text for the copied amplified sequence : useful to quickly locate the primers, when the sequence is pasted in an application which support styles

Corrections and improvements
- Adequacy of the use of the relation "Superior or equal to the cut off" for the drawing and the search for matches
- the use of right and left arrows, and the suppress key work in the « numeric-range » fields of the preferences’s window
- Correction of an error occuring while importing GeneBank format files.
- Correction of the display of information of the current selection of the sequence target at the time of the use of the menu "SelectAll", "lowercases", "uppercases" and while un-selecting
- Maintenance of the lower/uppercases features on the complementary strands
- Best updating of the “ default file “ radio-button state after a “ save as “ operation.
- When the window of search is displayed, the focus one is put into the field of search to avoid typing into the target sequence.
- Correction of a bug related to the list of the recent files preserved in the preference file and which could involve in certain circumstances a crash at AmplifX starting and whose only solution was yet to delete the preference file. - Correction of a bug that could occur if the quality scores had to be re-computed at the automatic loading of the primer’s default file.
- Correction of the placement of reverse primers over the chart (for small amplified fragments the primer length is not negligeable)

Jan. 9 2005 : Version 1.0

The First "Final" Release

Thanks to the suggestions and remarks of many users of the 0.9x versions I could improve AmplifX at a point it justify the version number of 1.00 !

New features or corrections
- New calculation of quality taking of account TM (bases stacking method), the %GC, the presence of polyX and the presence of dimers.
- New window drawer containing of the details on the primer quality and a field "observations" in order to associate any type of data text to each primer.
- The different matches from the same primer at several places on the sequence targets are now easily visualized by the simultaneous change of their color when the mouse flies over them.
- Taking into account of "U" (or u) in the targets and oligos - > automatically transformed into T (or t)
- Correction for the importation of text files of primers created with textEdit for example (nonconventional character of end of line for Mac)
- Translation of "contaminant" words in French in the English version (thank you to Todd Geders to have raised them and have proposed a translation)
- New table for the calculation of the score of annealing of the oligos : allows to better balance strong matching primers and weak matching ones.
- New and more readable drawings of the matches in two forms : strong (score > 170) and weak ones ; the same for amplified sequences drawings
- Primer or amplified fragment whose information tab are visualized are painted in a special color
- Choice is given to show weak matches a primer can get only if it have strong matches with the sequence or to show all weak matches.
- the columns "Length" and "Quality" of the list of primers are sortable by numerical size, the other columns remain sortable by alphanumeric order (Think of using string inputs of type Pr0001, Pr0002,... in field ID for example).
- The menu " open a sequence" is working :one can open sequence files in different text format like GenBank, EMBL,FastA, GCG. The other text formats being regarded as "rough" format i.e. all found « ATCGU »characters are being imported
- Improvement of the possibility of design the primers directly in AmplifX thanks to a live quality calculation while selecting nucleotides in the field "Target" (TM and global note of quality)
- « Select All » menu works with field « info »
- Horizontal scroll bar to change the visible area of the graphic area when it is zoomed in
- New menus : « Upper cases » and « Lower cases » to change the style of the current selection of the field « Target » (useful to visualize some parts into the graphic view and copy to another application)

Here is the list of all the nice guys that encourage me by their constructive remarks :

Jean-Paul Herman (my boss in my real job !), Jean-Louis Franc, Denis Becquet, Andrea Cabibbo, Christophe Hennequin, Corentin Cras-Méneur, Immo Junghärtchen, Jean-Paul Boissel, Markus Winter, Patrick Trieu-Cuot, Todd Geders.

Nov. 17 2004 : Version 0.96

Thanks to Patrick Cuot-Tieu who has reported an important bug and has suggested interesting evolutions.

- Correction of a bug in the selection boundaries of primer matches and amplified sequence in the target field (shift of 1 nucleotide)
- New text area above the target field showing the size and position in nucleotides of the current selection. (Particularly useful to design primers into AmplifX)
- New menu : « Paste complement strand » : to paste the complement of what is in the clipboard into the sequence column of the edited primer into the primer list. (Useful to design the reverse primer)
- Automatic copy of the true amplified sequence i.e. bordered by the primer sequences (useful when the primers don’t match completely the target, for example when restriction sites have been added to the 5’ end.)
- New « Register » menu to be alerted of new updates and to send feedback to the kind developer of this app.

Nov. 12 2004 : Version 0.95

Thanks to Immo Junghärtchen for helping me to debug and inprove interface and for helpful comments. Thanks to Denis Becquet too.

New features :
- Sequence primers are processed in the same manner than the target sequence : automatic cleaning of characters different from A,C,G,T
- Easy navigation into the primer list with tab and arrow keys.
- The primer list file name appears into a local menu at the top of the primer list. This allows an easy and fast loading of different favorite primer lists and more intuitive way to specify the default primer set (the one that is open automaticaly at the launching of the application)
- The primer list files have now a personalized icon and are double-clickable

- And a lot of bug corrections and code improvements

Nov. 2 2004 : Version 0.92

The First Public Release

AmplifX update. (0.92)

I would thank Immo Junghärtchen for very good comments that help (and motive) me to improve some aspects of amplifX.

New features :
- The main window of AmplifX is now resizable (Primer list columns also)
- Alert messages when one launches the PCR with no target sequence or no primer in list or no cheched primers.
- Cosmetic aspects of the main window have been fixed
- Fix window reactivation after “run PCR” execution.
- Help text corrected (thanks to Jean-Paul Herman)
- Best controls before opening or importing a primer list when a other primer list is yet loaded and has been modified.
- Other minor code improvements

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