It's easy to make your own TiddlyWiki that you can publish yourself - see how to SaveChanges for details. For more information and detiled instructions, read QuickStart.
TiddlyWiki is published under a BSD OpenSourceLicense that gives you the freedom to use it pretty much however you want, including for commercial purposes, as long as you keep my copyright notice. I'd appreciate a link back to http://www.tiddlywiki.com as well.\n\nThat license covers the TiddlyWiki //code//, any content you create when you are ReusingThisSite is as much yours as if you'd written it using MicrosoftWord.
As you can see in the RevisionHistory, I've been occasionally updating TiddlyWiki with bug fixes and minor new features. If you've been using an earlier revision of TiddlyWiki, here's how to upgrade to the latest version:\n* Open your TiddlyWiki file in FireFox (say it's called "mystuff.html")\n* SaveChanges to make sure that you've got a backup of it\n* Without closing that page, right-click on [[this link|http://www.personal.psu.edu/ach12/tiddlywiki/index.htm]], select 'Save target' or 'Save link' and save it as "mystuff.html", replacing your existing file\n* Now go back to the previously opened copy of "mystuff.html" in your browser and SaveChanges again. It will inherit the newly saved code\n* Refresh the page in the browser to verify that the upgrade has worked
Because QwikiWeb/TiddlyWiki is a single HTML file, you've actually already downloaded the entire software just by viewing this site. If you want to be able to SaveChanges, you can save your own TiddlyWiki to your local drive by right clicking on [[this link|#]] and selecting 'Save link as...' or 'Save target as...'. You can choose where to save the file, and what to call it (but keep a .HTM or .HTML extension). You can then use the DeleteAllTiddlers feature to delete all the existing content and start over.\n\nDo ''not'' use the File/Save command in your browser to save TiddlyWiki, because of SaveUnpredictabilities.
''Version 1.2.6 [ACH01] [May 11, 2005]''\n#EditMode: the page starts in standard mode with editing options disabled. By clicking the "advanced options" menu, the edit button and double-clicking-to-edit become available.\n#EditMode can be even further suppressed by placing a small file in the same directory as your wiki. For more information, read EditMode.\n#Other options -- such as save changes and interface options -- have been moved under the advanced menu.\n#Two new commands have been added: "create new tiddler" and "restart tiddlers." The latter command re-displays the site with just the DefaultTiddlers and is useful when making content changes. \n#HiddenTiddlers: this modification allows certain tiddlers (like SiteTitle and MainMenu) to be selectively hidden from both the Timeline and All tabs. This allows you to streamline your site's content while still having the hidden content available via search. Simply place the names of the tiddlers you wish to hide into the HiddenTiddlers entry.\n#Changed the search function for better forced search handling (i.e. in the original TiddlyWiki, if you did a search, then closed some of the tiddlers and wanted to get them back again, the search would not re-execute because the search phrase hadn't changed). Now whenever you click search or press Enter while in the search text field, the search will be re-executed.\n#NoSearchTiddlers: any tiddler title you place in this tiddler will be excluded from a search. Simply place the names of the tiddlers you wish to to exclude into the NoSearchTiddlers entry.\n#[[Tony Lownds'|http://tony.lownds.com/home/]] "config" modifications have been incorporated as "site settings" under advanced menu so as to provide easy access to those configuration tiddlers that might be set as HiddenTiddlers.\n#Several of [[Christian Hauck's|http://www.christianhauck.net/html/14300.html]] modifications have been incorporated including [[making the search box active on startup|http://www.christianhauck.net/html/14300.html#ChMig05]], [[delayed search|http://www.christianhauck.net/html/14300.html#ChMig07]] , and [[ExplicitTiddlers|http://www.christianhauck.net/html/14300.html#ChMig08]] (renamed from ExplicitTiddlerTitles to be consistent with other ConfigTiddlers names). The 8-digit number (LinkNum) portion of the ExplicitTiddlers mod has been omitted.\n#Tweaks to the CSS to accomodate the new commands & edit mode, and to offer a few color schemes. To see available color themes, read ColorThemes.
''Version 1.2.6 [ACH02] [May 12, 2005]''\n#''Enhancement:'' If you had "locked" out EditMode, then visitors would not have access to InterfaceOptions. Now if you lock EditMode, the "advanced options" link will be replaced with a simpler "interface options" link. For more information on locking, refer to EditMode.\n#''Enhancement:'' If NoSearchTiddlers does not exist, then the "exclude from search" feature will use the current or default entries for ConfigTiddlers. Default ConfigTiddlers include: SiteTitle, SiteSubtitle, MainMenu, DefaultTiddlers, ConfigTiddlers, HiddenTiddlers, and NoSearchTiddlers.\n
''Version 1.2.8 [ACH03] [May 17, 2005]''\n#''Enhancement:'' Incorporated JeremyRuston's version 1.2.8 updates including:\n**CustomStyleSheet support\n**Modifications to SaveChanges routine (i.e. subsequent saves)\n**Support for AutoSave and SaveBackups\n**Other minor code changes\n#Changed the "save changes" routine so that the backup files use the same file extension as the original file (.html or .htm). Before this change, the backups had ".html" hard-coded to the filename.\n#Renamed this member of the TiddlyWikiAdaptations family to "QwikiWeb" so as to set it apart from other adaptations in online discussions.
#displayArea {background-color: #ffccff; }\n#mainMenu {border: 1px solid #ffff88; }\n#commandPanel {background-color: #008800; }
You can skin TiddlyWiki with a special StyleSheet tiddler containing your own CSS style sheet declarations. Unlike hacking the HTML directly, the StyleSheet tiddler withstands upgrading to a new version of the TiddlyWiki code (see HowToUpgrade).\n\nThe ExampleStyleSheet shows some of the basic options you can control. SaveChanges and then click refresh in your browser to see StyleSheet changes. Any errors in your CSS syntax will be caught and displayed, but they shouldn't stop TiddlyWiki from working.
InterfaceOptions are displayed when you click the 'options' button on the right. They are saved in a cookie on your browser, making them sticky between visits. RegExpSearch allows more complex search expressions; CaseSensitiveSearch does as it's name implies. The user name for edits should be set //before// starting to edit things (ouch. another bug). AutoSave and SaveBackups give the option of automatically saving changes and whether to generate backup files. You can also choose to GenerateAnRssFeed.
To use QwikiWeb as the basis for your website, follow these instructions:\n#Download a copy of the html file by right-clicking on [[this link|#]] and selecting 'Save link as...' or 'Save target as...'. You can choose where to save the file, and what to call it (but keep the .HTML or .HTM extension).\n#Open up the copy of the file you just saved and begin making your content changes. To add or delete tiddlers, make sure that the advanced options are showing.\n''Note:'' you can now use a special command to quickly delete the existing site content and start over with a completely blank copy of QwikiWeb. For more information, read DeleteAllTiddlers.\n#Use the "save changes" command to make your changes permanent. It is a good idea to use this command periodically (or turn on the AutoSave feature) when making numerous changes at one sitting.\n#Now upload the copy of the file saved on your computer to your website. You will need to check with your hosting provider or ISP to determine where your page must be saved and what it should be named.\n#Verify that you can access the website file from the internet.\n#If you want to make additional changes, simply edit the copy of QwikiWeb on your computer and re-upload it to your website.\n#And you can customize the look and feel of QwikiWeb using ColorThemes, StickySettings, and the CustomStyleSheet.
''Version 1.2.9 [ACH04] [May 18, 2005]''\n#''Enhancement:'' Incorporated JeremyRuston's version 1.2.9 updates including:\n**GenerateAnRssFeed with a slight modification so that HiddenTiddlers do not get published to the RssFeed (also streamlined the HiddenTiddlers function to work better with Jeremy's new code)\n**Changed the CustomStyleSheet feature for better Safari compatibility\n**Other minor code changes (see Jeremy's RevisionHistory for more details)\n#''Enhancement:'' Changed SaveChanges so that the last 'div' tag gets wrapped to it's own line (a slight bug in the original that always bothered me when needing to copy and paste stores). If you don't know anything about this issue, don't worry...it won't affect your use of TiddlyWiki/QwikiWeb in any way.\n#I'm still trying to simplify using Jeremy's new CustomStyleSheet feature to create new themes. I need to explore this issue further, but my ColorThemes approach still works for now.
''Version 1.2.12 [ACH05] [May 26, 2005]''\n#''Enhancement:'' Incorporated JeremyRuston's changes in the 1.2.12 release, including SaveEmptyTemplate, MonospacedText, and other fixes (for more information, read Jeremy's RevisionHistory).\n#''Bugfix:'' fixed an issue with the DeleteAllTiddlers feature that prevented the empty TiddlyWiki from loading properly in the browser (caused by an empty or non-existant ExplicitTiddlers tiddler). Now QwikiWeb will work even when the ExplicitTiddlers entry is empty or non-existant.\n#''Enhancement:'' Added a new option item to ShowHiddenTiddlers so that editors can view the entire website contents for easy access to HiddenTiddlers. ''Note:'' if ShowHiddenTiddlers is enabled, then HiddenTiddlers will also be published to the RssFeed.\n#''Tweak:'' I liked the way Jeremy's previous versions saved the html stores with the newest ones at the bottom. In version 1.2.10-1.2.12, that switched to saving the newest ones at the top. I restored the original save order while still keeping newest items at the top when saving the RssFeed.\n#FYI, I noticed that using the new MonospacedText option with blocks of text does not display properly under IE.
If you have used the HiddenTiddlers feature to hide some of your content, you can check the option to ShowHiddenTiddlers to temporarily show ''all'' tiddler content. In order for the hidden content to show, you must be in EditMode (i.e. the advanced options must be showing). This "catch" allows you to lock down all HiddenTiddlers by using UserMode to disable access to EditMode while the file is being viewed from a web server.\n\nBe aware that if you GenerateAnRssFeed while ShowHiddenTiddlers is checked, any HiddenTiddlers will be published to the RssFeed. To publish only the visible tiddlers, uncheck the ShowHiddenTiddlers option before saving the RssFeed.
The addition of AutoSave to the InterfaceOptions causes TiddlyWiki to automatically perform a SaveChanges each time you edit a tiddler, making it a good deal harder to accidentally lose information. However, if you also choose to SaveBackups you will end up generating an awful lot of files...
By WebsiteOriented, I mean that it is easy and effective to use QwikiWeb as a method for publishing your own website. TiddlyWiki works great for this because all of your site's MicroContent is housed in one single html file, making it easy to upload your content revisions. In fact, the only time that additional files are required is when you choose to insert an image or link to an external file or document. Then you need to upload the respective files as well as the altered QwikiWeb file.\n\nThe QwikiWeb adaptation of TiddlyWiki takes a great idea and makes it even better for WebsiteOriented use. Here are a few of the enhancements that make QwikiWeb a useful adaptation:\n*An EditMode which can be toggled on and off or even "locked down" to visitors of your website\n*The ability to mark content which is hidden and does not show up on the Timeline/All tabs. Tiddlers like SiteTitle, MainMenu, and DefaultTiddlers are perfect examples as is the ExtendedFormatting tiddler. You want them there so that you can access them, but you don't want visitors seeing them.\n* The option to excluded certain tiddlers from showing up in the search results (probably for the same reasons you might want make them hidden).\n*Additional improvements that have been gleaned from other TiddlyWikiAdaptations. For more information on all these changes, read the RevisionHistoryACH.
NoSearchTiddlers are one of the SpecialTiddlers. It allows you to block specific tiddlers from showing up in the search results. Simply add the title of the tiddler you wish to block to a tiddler called NoSearchTiddlers and the feature will be activated. For example, adding "MainMenu" to the NoSearchTiddlers tiddler will ensure that the MainMenu tiddler does not show up in the results of a user search.
I live near Philadelphia, Pennsylvania, U.S. and work for The Pennsylvania State University at its [[Abington|http://www.abington.psu.edu]] location.\n\nOne day, while looking for a server-side Wiki solution, I discovered TiddlyWiki listed on a [[spur.net|http://www.spurl.net/saved/saved_8205_1101447905.htm]] page. I was so amazed that JeremyRuston was able to build an entire Wiki into a single html/javascript file that I downloaded it and started experimenting with some additional features and options. QwikiWeb is the result. I am truly indebted to Jeremy for creating TiddlyWiki and sharing it under a BSD open license.
''Attention Coders:''\nIf you would like to incorporate some or all of the code modifications in QwikiWeb, you may want to look at the latest [[CodeDifference|codediff.htm]] page. It will help you identify exactly what was changed/added in TiddlyWiki to create QwikiWeb.
If you are wanting to use QwikiWeb for your own website, there is an easy way to delete all the existing tiddler content and start over with a blank copy. This option should be used with caution as it will erase every tiddler in the existing file. \n\n''How to DeleteAllTiddlers:''\n#Make sure that you have downloaded the QwikiWeb file and are viewing that copy on your computer\n#Make sure that you are in EditMode by clicking on the "show advanced options" command. The DeleteAllTiddlers feature will not activate if EditMode is not enabled.\n#Use the save changes command so that you have a backup of the tiddler content (enable backups if necessary)\n#Click in the search box and type in the phrase DeleteAllContent\n#You will be asked to confirm that you want to delete the tiddler content; click OK to proceed\n#All tiddlers will be deleted, and you will be presented with a screen where you can setup new values for the site title, subtitle, main menu, etc.\n#When you have completed your edits, save the changes again to preserve your new content
There are times when you need to have a tiddler, but you don't want to make it visible to your web visitors. You can use one of the SpecialTiddlers called HiddenTiddlers to identify any tiddler titles that you don't want to show in the first two sidebar tab listings. For example, by placing the titles "SiteSubtitle" and "MainMenu" in HiddenTiddlers, they will not display in the Timeline or All tabs. \n\nThere is a checkbox under the interface options to ShowHiddenTiddlers, allowing instant access to all hidden items. Additionally, HiddenTiddlers will not be published to the RssFeed and will not show up as tiddler references (under each tiddler's "references" button) unless the ShowHiddenTiddlers option is enabled.\n\nMaking a tiddler hidden does not affect the search function, so you can use search to quickly find a specific tiddler. If you want to hide a tiddler from showing up in the search results, use the ExcludeFromSearch feature.
TiddlyWiki is the creation of JeremyRuston who was kind enough to share it under an OpenSourceLicense.\n\nA TiddlyWiki is like a blog because it's divided up into neat little chunks, but it encourages you to read it by hyperlinking rather than sequentially: if you like, a non-linear blog analogue that binds the individual microcontent items into a cohesive whole. There are also several other adaptations of TiddlyWiki like QwikiWeb that were written by other developers based on earlier versions of TiddlyWiki.\n\n*Here are some links to some other important TiddlyWiki information:\n**[[MainFeatures|http://www.tiddlywiki.com#MainFeatures]]\n**ReusingThisSite\n**SaveChanges\n**KnownBugs\n\nFor more information, visit the TiddlyWiki website at http://www.tiddlywiki.com.
This is one of the InterfaceOptions you can use to customize TiddlyWiki. It determines whether TiddlyWiki creates a backup file each time you SaveChanges. I'd suggest keeping it switched on for safety!
''Old QwikiWeb revision highlights:''\nThe following modifications were added by AlanHecht:\n----\n|bgcolor(#d0d0d0):Info on TiddlyWiki code changes can be found at http://www.osmosoft.com/#RevisionHistory|\n*''Version 1.2.14 [ach06b] [June 7, 2005]''\n**Fixed a problem where clicking an "edit" button caused an error in IE\n\n*''Version 1.2.14 [ACH06] [June 4, 2005]''\n(//for more details read// ACH06)\n**Added integrated support for SpellBound SpellChecking\n**Added a DuplicateTiddler button to the editor toolbar\n**Added ForceEditMode feature\n\n*''Version 1.2.14 [ach05b] [May 31, 2005]''\n**Incorporated JeremyRuston's changes in the 1.2.14 release\n\n*''Version 1.2.12 [ACH05] [May 26, 2005]''\n(//for more details read// ACH05)\n**Incorporated JeremyRuston's changes in the 1.2.12 release\n**Fixed an issue with the DeleteAllTiddlers feature\n**Added an option item to always ShowHiddenTiddlers\n\n*''Version 1.2.9 [ach04b] [May 19, 2005]''\n**Added the DeleteAllTiddlers feature\n\n*''Version 1.2.9 [ACH04] [May 18, 2005]''\n(//for more details read// ACH04)\n**Incorporated JeremyRuston's changes in the 1.2.9 release, including GenerateAnRssFeed\n**Adjusted the RssFeed feature so that it does not publish HiddenTiddlers\n\n*''Version 1.2.8 [ACH03] [May 17, 2005]''\n(//for more details read// ACH03)\n**Incorporated JeremyRuston's changes in both the 1.2.7 and 1.2.8 releases\n**Changed "save changes" so that the backup files use the same file extension as the original file (.html or .htm)\n**Slight tiddler content changes\n\n*''Version 1.2.6 [ACH02] [May 12, 2005]''\n(//for more details read// ACH02)\n**Improvements to the "locked" mode and NoSearchTiddlers feature\n\n*''Version 1.2.6 [ACH01] [May 11, 2005]''\n(//for more details read// ACH01)\n**Added an EditMode that can be toggled on/off and the HiddenTiddlers & NoSearchTiddlers features\n**Added new commands for creating new tiddlers, restarting DefaultTiddlers, and accessing the site settings\n**Added many of [[Christian Hauck's|http://www.christianhauck.net/html/14300.html]] modifications\n**Created several ColorThemes
If you are using FireFox to edit your QwikiWeb, you can take advantage of a FireFoxExtension called SpellBound which allows you to check the spelling of any text input field on a web page. Beginning with version [[ACH06]], QwikiWeb has integrated support for SpellBound directly into the editing toolbar.\n\nTo use SpellChecking, first confirm that SpellBound is installed and working properly. Then when you edit a tiddler, follow these simple steps:\n#Manually click your mouse in the text input area of the tiddler to signal to SpellBound that this is the field it should spellcheck @@color(#ff0000):''(this is very important)''@@\n#Click the @@color(#606060):''spellcheck''@@ button in the editor toolbar\n\nA pop-up window will give you options to ignore mispelled words, add them to the personal dictionary, or replace them based on SpellBound's word suggestions.
You can click the ''duplicate'' button on a tiddler's edit toolbar to create an exact copy of the original tiddler. This is useful if you want to base new diary entries on a template or have a new tiddler that is similar in format to an existing one.\n\nTo differentiate the new duplicate from the original, the word {{{''Copy''}}} is added to the end of the original tiddler's title.\n\n''Note:'' if you do a lot of duplicating, you can move the duplicate button from the editor toolbar to the standard toolbar (for quicker access) by editing QwikiWeb's source code.
A FireFoxExtension is a downloadable piece of software that adds new functionality to the FireFox web browser. To learn more about extensions and to download the latest extensions, visit the [[FireFox Extension page|https://addons.mozilla.org/extensions/?application=firefox]].
EditMode can be totally suppressed to web vistors by placing a small javascript file in the same directory as your wiki html file on your web server. To get a copy of the javascript file, right-click this [[locked.js|http://www.personal.psu.edu/ach12/tiddlywiki/js/locked.js]] link and save the file to your computer. \n*Locking EditMode will also:\n**Hide the advanced options link entirely and replace it with an InterfaceOptions link\n**Hide the options under InterfaceOptions that only apply when editing & saving tiddler content (e.g. SaveBackups, AutoSave, GenerateAnRssFeed, etc.)\n\n''Note:'' if you have this LockEditMode file and the ForceEditMode file both in the same folder as the html file, then the ForceEditMode will take precedence.
Because EditMode can be toggled on and off in QwikiWeb, reloading the page in between edits may get frustrating as you will have to repeatedly toggle EditMode back on every time the page reloads. You can now ForceEditMode to stay on by placing the [[forced.js|http://www.personal.psu.edu/ach12/tiddlywiki/js/forced.js]] file in the same folder on your hard drive that you use for the QwikiWeb html file.\n\nWhen QwikiWeb sees the forced.js file in the same folder, it always loads the web page with EditMode turned on.\n\n''Note:'' if you have this ForceEditMode file and the LockEditMode file both in the same folder as the html file, then the ForceEditMode will take precedence.
EditMode can be turned on to enable editing of wiki content and settings. Use the "show/hide advanced options" to toggle EditMode on and off. ''Note:'' the site starts with EditMode turned off to simplfy the interface for new site visitors.\n*With EditMode Off:\n**Edit button does not appear in the tiddler toolbars\n**Double-clicking to edit tiddlers is disabled\n**Interface options and other advanced settings are replaced by a simpler options list\n\n*With EditMode On:\n**Edit button is visible in the tiddler toolbars\n**Double-clicking to edit tiddlers is enabled\n**Additional commands appear in the menu (features like: interface options, create new tiddler, site settings, and save changes)\n\nYou can also LockEditMode on a webserver to keep visitors from seeing EditMode at all, or you can ForceEditMode to stay on for faster access to the editing options.
SpellBound was chosen for QwikiWeb's SpellChecking capability for several reasons:\n\nSpellBound...\n#Uses the same language dictionaries as Mozilla Thunderbird. Currently there are over 45 international language [[dictionaries|http://dictionaries.mozdev.org/installation.html]] available which means that most international users can take advantage of SpellChecking\n#Includes a personal dictionary that is kept on your local computer. This means that you can choose to add a common WikiWord to your dictionary so that it will not get flagged on subsequent spell checks (a real time saver)\n#Doesn't try to spell check a URL and other ExtendedFormatting it encounters (another time saver)\n#Is available for Windows, Mac OS X, Linux, and a few other operating systems, so this one solution can meet the needs of most people\n#Does not require a web server or an Internet connection in order to work; once the spell checker and dictionary are installed on your system, you are all set to go\n#Is easy for the end user to install since the spell checker and dictionaries are each available as a FireFoxExtension\n#Doesn't add unwanted bloat to the QwikiWeb/TiddlyWiki code\n#Is free! Read SpellBound for more information.\n\nIf you know of a better approach that meets all of these requirements, by all means EmailMe.\n\n|bgcolor(#d0d0d0):FYI, SpellBound cannot check the whole html document in one pass (not yet anyway), and SpellBound requires that you manually click in the tiddler's edit textarea ''before'' you click the spellcheck button, but those are things I can live with for now.|
SpellBound is a FireFoxExtension that provides comprehensive spellchecking for any text field on any web page you visit. You can use SpellBound to check the spelling of an e-mail message sent from a web interface or a message being posted to a blog or message forum. Most importantly, you can use SpellBound to check the spelling of your QwikiWeb tiddlers using the SpellChecking feature. Visit http://spellbound.sourceforge.net for more information and installation instructions.\n\n*For more detail on why the SpellBound approach was used for QwikiWeb, read WhyUseSpellBound.\n\n*''Additonal Notes:''\n**If you have recently upgraded FireFox and now SpellBound doesn't seem to work, you may have to re-install SpellBound and your dictionaries [[more info|http://spellbound.sourceforge.net/faq#q601]]\n**The author of SpellBound indicates that the method used here to activate the spell checker may be changed in future versions. I will endeavor to keep up to date with future SpellBound releases.
''Version 1.2.14 [ACH06] [June 4, 2005]''\n#''Enhancement:'' Added integrated support for SpellChecking using the SpellBound FireFoxExtension. The SpellChecking button is visible when you are editing a tiddler. SpellBound is a great extension, but it is somewhat limited in terms of what it can do. Please don't send me emails requesting things like, "I'd like to spell check the whole database of tiddlers at one time," etc. Until SpellBound is updated, there's not much I can do. For more information, read WhyUseSpellBound.\n#''Enhancement:'' Added a new DuplicateTiddler button to the editor toolbar that allows you to use an existing tiddler as a template for a new tiddler\n#''Tweak:'' Added some comment lines to the external ''locked.js'' file for locking EditMode so that users will know what to do with it. For more information, read LockEditMode.\n#''Tweak:'' Created another external javascript file that will force EditMode to stay on if it is in the same local directory as the QwikiWeb html file. For more information, read ForceEditMode.
You can SaveChanges if you're using FireFox or InternetExplorer:\n# if you're using Windows XP you might run into ServicePack2Problems\n# right click on [[this link|#]] and select 'Save link as...' or 'Save target as...'\n** do ''not'' try to use the File/Save command in your browser because of SaveUnpredictabilities.\n** choose where to save the file, and what to call it (but keep an .HTM or .HTML extension)\n# open the newly downloaded file in your browser\n# click the 'options' button on the right to set your username\n# edit, create and delete the tiddlers you want\n** you can change the SpecialTiddlers to change the SiteTitle and MainMenu etc.\n# click the 'save changes' button under the advanced options on the right to save your changes\n# TiddlyWiki will make a backup copy of the existing file (if the backup option is checked), and then replace it with the new version\n
QwikiWeb is built on recent versions of JeremyRuston's TiddlyWiki. But in addition to the basic TiddlyWiki functions and features, AlanHecht has added the following (click on each feature link to read more):\n#A LanguageOverlay for setting your own text and language for all buttons and messages\n#ColorThemes which make customizing the look QwikiWeb very easy\n#UserMode to set the level of difficulty for the display interface\n#Additional buttons for duplicating tiddlers, creating new tiddlers, close all other tiddlers, and collapse/expand a tiddler\n#Integrated SpellChecking support\n#ExcludeFromSearch\n#HidingTiddlers with HiddenTiddlers\n#A SiteSettings page\n#EditMode\n#A DeleteAllTiddlers command that lets you start over with a blank QwikiWeb instantly\n#And much more. Read RevisionHighlights for more detail.\n
*If you wish to contact AlanHecht regarding QwikiWeb (my adaptation of TiddlyWiki), the email address is //''ach12 (at) psu (dot) edu''//\n\n*To contact JeremyRuston (the originator of TiddlyWiki), his email address is\n//''jeremy (at) osmosoft (dot) com''//
MainMenu SiteTitle SiteSubtitle SpecialCharacters
These known bugs are with QwikiWeb. For more information on KnownBugs with TiddllyWiki, visit http://tiddlywiki.com#KnownBugs.\n\nNone at this time (but I'm sure you all will let me know).
The original TiddlyWiki code by JeremyRuston is ©2005 by [[osmosoft|http://www.osmosoft.com]].\n\nThe QwikiWeb code additions are ©2005 by AlanHecht.
The ColorThemes feature has changes. Now you can use the SpecialTiddler called ColorTheme to easily set a new color scheme for QwikiWeb. ColorTheme is predefined with only a few colors that need to be selected. Based on your choices, other elements will be adjusted to use those same colors. To see what your color settings look like, edit and save the ColorTheme tiddler, then SaveChanges. When you reload the page, you should see the new ColorTheme in place.\n\nThere are also a few template ColorTheme samples:\n• ColorThemeBlue\n• ColorThemeEmpty (one just waiting for you to fill it out with your own colors)\n\nTo use one of these, you will have to rename the current ColorTheme to another title, and then rename ColorThemeBlue to ColorTheme.
To find special characters that can be used in QwikiWeb using HTML character codes or by copy/pasting the character into LingoInterface, visit http://www.tntluoma.com/sidebars/codes or search the web for "HTML character entities."\n\n
The LanguageOverlay allows users to customize the wording for the QwikiWeb interface and pop-up alerts. The LanguageOverlay is broken into two parts:\n#LingoInterface - used to customize buttons and the hover text for items that appear on the page\n#LingoMessages - used to customize messages and pop-ups that are longer and are usually only visible after some action has taken place\n\n|Here are some additional details about how the LanguageOverlay system works:|\n*The default English interface and messages are hardcoded into QwikiWeb and will survive even if the LingoInterface and LingoMessages tiddlers are deleted\n*The syntax of LingoInterface and LingoMessages are slightly different. LingoInterface puts each item on it's own line that includes an equals sign ("="). In LingoMessages, you must separate each customized message with two tilde ("~") characters. This is due to the fact that //messages// can themselves contain line feeds or hard returns.\n*For any item in LingoInterface or LingoMessages that is left blank or deleted entirely from the tiddler, QwikiWeb will revert back to the hardcoded English default for that item\n*In order for edits to LingoInterface and LingoMessages to take effect, you must "save changes" and reload the file in the browser
UserMode is one of the sets of options listed under StickySettings. It allows the QwikiWeb author to define a set of viewing options that define how the QwikiWeb interface will look. You are allowed to define two UserMode groups:\n#''userModeWeb'' defines how the wiki will appear to anyone viewing the page from the web\n#''userModeLocal'' defines how the wiki will appear when it is saved to either a local computer or a mapped hard drive\n\nThere are a few mode options as well, from full editor rights to more simple interface modes. There is even a custom mode that lets you define a specific set of options by copying and pasting pre-programmed lines of javascript code. \n\nFor more information, read StickySettings.
''Version 1.2.19 [ACH07b] [June 14, 2005]''\n#''Code Update:'' Incorporated JeremyRuston's changes in the 1.2.16-1.2.19 releases\n#''Tweak:'' Tweaked the MoreTab so it is only visible while in EditMode (so it can be hidden from web visitors)\n#''Enhancement:'' Added a LanguageOverlay system which allows the wording for the entire QwikiWeb interface to be drawn from tiddlers. This also means that any language changes you make will survive an upgrade to the latest code version. The Language Overlay is broken down into two tiddler: LingoInterface and LingoMessages.\n#''Enhancement:'' Added a new feature called UserMode that allows the author to select how the interface looks. There is one viewing mode for viewing this file online and one for viewing it locally. This feature replaces the previous LockEditMode & ForceEditMode which required external javascript files.\n#''Enhancement:'' ColorThemes can now be personalized. Instead of me publishing a few different color scheme versions of the same QwikiWeb release, there is now a tiddler called ColorTheme. ColorTheme works similar to the CustomStyleSheet except that all you do is define a few basic colors. It's called a "theme" because the same color selection is often used for multiple aspects of the web page. This makes ColorTheme much simpler and easier for novices to use than actual the CSS of a StyleSheet. There are several themes already defined: ColorThemeBlue, ColorThemeCranberry, and ColorThemeTeal. Simple rename any of them to "ColorTheme," save changes, and reload to see the theme applied. ''Note:'' A ColorTheme gets applied before the CustomStyleSheet tiddler, so you can still tweak additional settings using full CSS.\n#''Enhancement:'' Added two new buttons to the tiddler toolbar: "collapse/expand" and "close others." While the ideas for having these came from other TiddlyWiki adaptations, the code implementation is my own and much simpler.\n#''Enhancement:'' Added an option after using DeleteAllTiddlers to reinsert the directions tiddler for future use (since that feature is not documented elsewhere). If the DeleteAllTiddlers tiddler no longer exists, then a default English version is created.\n#''Tweak:'' Optimized some of the original QwikiWeb code to enhance performance and decrease size. The newest code has not been optimized yet, but will be in the future.\n#''Tiddler Content Changes:'' Removed most of the original TiddlyWiki content to save space and concentrate on what makes QwikiWeb unique. If you want help with Using TiddlyWiki features, visit the original [[TiddlyWiki Website|http://www.osmosoft.com/]].
|!To use this theme, you must rename its tiddler title to ColorTheme|\n''You can use either ColorNames or HexCodes to define the following colors:''\n\n|The ''Background'' color for the main reading area of the page|\n:colBackground=\n\n|The ''Banner'' color is also used for WikiWord links and the sidebar commands text|\n:colBanner=#800040\n\n|SiteTitle text color|\n:colSiteTitle=#fefebf\n\n|SiteSubtitle text color|\n:colSiteSubtitle=#ff8080\n\n|SiteTitle/SiteSubtitle link color|\n:colTitleLineLinks=#fefebf\n\n|SiteTitle/SiteSubtitle link color on mouse hover|\n:colTitleLineLinksOnHover=white\n\n|The ''menu'' background color is also used for links in the title/subtitle, toolbar buttons color, the tiddler links in the sidebar tabs, and the references button pop-up|\n:colMainMenu=#fefebf\n\n|The ''sidebar'' background color is also used for hyperlinks and wiki words in the title/subtitle, and the toolbar button text, and the toolbar buttons on mouse hover|\n:colSidebar=#400040\n\n|Sidebar commands link text color (search, etc.)|\n:colSidebarCommands=white\n\n|Timeline tab background|\n:colTabTimeline=#800040\n\n|Date sub-headings for the Timeline tab|\n:colTimelineHeadings=#ff8080\n\n|All tab background|\n:colTabAll=#a9055b\n\n|More tab background|\n:colTabMore=#ac027d\n\n|The text color used for the body text of tiddlers when they are visible|\n:colTiddlerText=\n\n|The ''Deselected Tiddler'' color is used when the mouse is not hovering over a tiddler|\n:colDeselectedTiddler= \n\n|The ''Selected Tiddler'' color is used when the mouse is hovering over a tiddler|\n:colSelectedTiddler=#ffffef\n\n|The ''Animation'' color is used for the animated box that grows and scrolls when a tiddler opens|\n:colAnimation=#FF8080\n\n|Text color for ExtendedFormatting Headers|\n:colHeaderText=#800040\n\n|Background color for ExtendedFormatting Headers|\n:colHeaderBackground=#FF8080\n\n|Text color for Table Header Cells|\n:colTableHeaderText=#800040\n\n|Background color for Table Header Cells|\n:colTableHeaderBackground=#FF8080\n\n|If you want to change the color or style of anything more specific, you can use the CustomStyleSheet|
|!To use this theme, you must rename its tiddler title to ColorTheme|\n''You can use either ColorNames or HexCodes to define the following colors:''\n\n|The ''Background'' color for the main reading area of the page|\n:colBackground=\n\n|The ''Banner'' color is also used for WikiWord links and the sidebar commands text|\n:colBanner=#000080\n\n|SiteTitle text color|\n:colSiteTitle=#b5b7f5\n\n|SiteSubtitle text color|\n:colSiteSubtitle=white\n\n|SiteTitle/SiteSubtitle link color|\n:colTitleLineLinks=#4455EE\n\n|SiteTitle/SiteSubtitle link color on mouse hover|\n:colTitleLineLinksOnHover=#b5b7f5\n|The ''menu'' background color is also used for links in the title/subtitle, toolbar buttons color, the tiddler links in the sidebar tabs, and the references button pop-up|\n:colMainMenu=#fefebf\n\n|The ''sidebar'' background color is also used for hyperlinks and wiki words in the title/subtitle, and the toolbar button text, and the toolbar buttons on mouse hover|\n:colSidebar=#b5b7f5\n\n|Sidebar commands link text color (search, etc.)|\n:colSidebarCommands=#000080\n\n|Timeline tab background|\n:colTabTimeline=#4455EE\n\n|Date sub-headings for the Timeline tab|\n:colTimelineHeadings=#000030\n\n|All tab background|\n:colTabAll=#000080\n\n|More tab background|\n:colTabMore=#2001cd\n\n|The text color used for the body text of tiddlers when they are visible|\n:colTiddlerText=\n\n|The ''Deselected Tiddler'' color is used when the mouse is not hovering over a tiddler|\n:colDeselectedTiddler= \n\n|The ''Selected Tiddler'' color is used when the mouse is hovering over a tiddler|\n:colSelectedTiddler=#ffffef\n\n|The ''Animation'' color is used for the animated box that grows and scrolls when a tiddler opens|\n:colAnimation=#b5b7f5\n\n|Text color for ExtendedFormatting Headers|\n:colHeaderText=#000080\n\n|Background color for ExtendedFormatting Headers|\n:colHeaderBackground=#b5b7f5\n\n|Text color for Table Header Cells|\n:colTableHeaderText=#000080\n\n|Background color for Table Header Cells|\n:colTableHeaderBackground=#b5b7f5\n\n|If you want to change the color or style of anything more specific, you can use the CustomStyleSheet|
|!To use this theme, you must rename its tiddler title to ColorTheme|\n''You can use either ColorNames or HexCodes to define the following colors:''\n\n|The ''Background'' color for the main reading area of the page|\n:colBackground=\n\n|The ''Banner'' color is also used for WikiWord links and the sidebar commands text|\n:colBanner=#005050\n\n|SiteTitle text color|\n:colSiteTitle=#fefebf\n\n|SiteSubtitle text color|\n:colSiteSubtitle=white\n\n|SiteTitle/SiteSubtitle link color|\n:colTitleLineLinks=#fefebf\n\n|SiteTitle/SiteSubtitle link color on mouse hover|\n:colTitleLineLinksOnHover=#008080\n\n|The ''menu'' background color is also used for links in the title/subtitle, toolbar buttons color, the tiddler links in the sidebar tabs, and the references button pop-up|\n:colMainMenu=#fefebf\n\n|The ''sidebar'' background color is also used for hyperlinks and wiki words in the title/subtitle, and the toolbar button text, and the toolbar buttons on mouse hover|\n:colSidebar=#fefebf\n\n|Sidebar commands link text color (search, etc.)|\n:colSidebarCommands=#005050\n\n|Timeline tab background|\n:colTabTimeline=#008080\n\n|Date sub-headings for the Timeline tab|\n:colTimelineHeadings=#000030\n\n|All tab background|\n:colTabAll=#005050\n\n|More tab background|\n:colTabMore=#883900\n\n|The text color used for the body text of tiddlers when they are visible|\n:colTiddlerText=\n\n|The ''Deselected Tiddler'' color is used when the mouse is not hovering over a tiddler|\n:colDeselectedTiddler= \n\n|The ''Selected Tiddler'' color is used when the mouse is hovering over a tiddler|\n:colSelectedTiddler=#ffffef\n\n|The ''Animation'' color is used for the animated box that grows and scrolls when a tiddler opens|\n:colAnimation=#b5b7f5\n\n|Text color for ExtendedFormatting Headers|\n:colHeaderText=#005050\n\n|Background color for ExtendedFormatting Headers|\n:colHeaderBackground=#7CC7CB\n\n|Text color for Table Header Cells|\n:colTableHeaderText=#005050\n\n|Background color for Table Header Cells|\n:colTableHeaderBackground=#7CC7CB\n\n|If you want to change the color or style of anything more specific, you can use the CustomStyleSheet|
|!To use this theme, you must rename its tiddler title to ColorTheme|\n''You can use either ColorNames or HexCodes to define the following colors:''\n\n|The ''Background'' color for the main reading area of the page|\n:colBackground=\n\n|The ''Banner'' color is also used for WikiWord links and the sidebar commands text|\n:colBanner=\n\n|SiteTitle text color|\n:colSiteTitle=\n\n|SiteSubtitle text color|\n:colSiteSubtitle=\n\n|SiteTitle/SiteSubtitle link color|\n:colTitleLineLinks=\n\n|SiteTitle/SiteSubtitle link color on mouse hover|\n:colTitleLineLinksOnHover=\n\n|The ''menu'' background color is also used for links in the title/subtitle, toolbar buttons color, the tiddler links in the sidebar tabs, and the references button pop-up|\n:colMainMenu=\n\n|The ''sidebar'' background color is also used for hyperlinks and wiki words in the title/subtitle, and the toolbar button text, and the toolbar buttons on mouse hover|\n:colSidebar=\n\n|Sidebar commands link text color (search, etc.)|\n:colSidebarCommands=\n\n|Timeline tab background|\n:colTabTimeline=\n\n|Date sub-headings for the Timeline tab|\n:colTimelineHeadings=\n\n|All tab background|\n:colTabAll=\n\n|More tab background|\n:colTabMore=\n\n|The text color used for the body text of tiddlers when they are visible|\n:colTiddlerText=\n\n|The ''Deselected Tiddler'' color is used when the mouse is not hovering over a tiddler|\n:colDeselectedTiddler= \n\n|The ''Selected Tiddler'' color is used when the mouse is hovering over a tiddler|\n:colSelectedTiddler=\n\n|The ''Animation'' color is used for the animated box that grows and scrolls when a tiddler opens|\n:colAnimation=\n\n|Text color for ExtendedFormatting Headers|\n:colHeaderText=\n\n|Background color for ExtendedFormatting Headers|\n:colHeaderBackground=\n\n|Text color for Table Header Cells|\n:colTableHeaderText=\n\n|Background color for Table Header Cells|\n:colTableHeaderBackground=\n\n|If you want to change the color or style of anything more specific, you can use the CustomStyleSheet|
Because you might be upgrading from a previous code set of QwikiWeb and still using your own tiddlers, you may need to add or change some of the content in one or more SpecialTiddlers that QwikiWeb uses to configure certain aspects of the page. The following list identifies any tiddler changes that should be replicated in your existing tiddlers:\n|!QwikiWeb version|!Release Date|!Tiddler Affected|!Change Summary|\n|ach07f|June 16, 2005|LingoInterface|''Added '':btnExpandTitle and also changed the default text for both :btnCollapseTitle and :btnExpandTitle so that they are totally indepent (previously, the default text was combined as "Collapse/expand this tiddler"). Also added an option called :varNumRssItems that lets you customize the number of most recent tiddlers published to the RssFeed.|\n|||ColorTheme|''Added '' separate new elements for the command text in the sidebar, and title/subtitle links and hover links.|\n|ach07i|June 24, 2005|LingoMessages|''Added '':msgMissingNewTiddler that sets the default instructions that appear when a non-exisiting tiddler link is clicked.|\n
Several adaptations of TiddlyWiki have been developed. The purpose of this adaptation (called QwikiWeb) is to improve the look and feel of TiddlyWiki when used as the basis for a public web site. New CSS has been used and several features have been added that allow for a more WebsiteOriented experience. \n*If you don't know what TiddlyWiki is, you should visit http://www.tiddlywiki.com first. Once you understand what it is, QwikiWeb will make more sense.\n*For more information on the differences between TiddlyWiki and QwikiWeb, read AddedFeatures\n*For instructions on using QwikiWeb for a website, read QuickStart\n*You can be notified about updates to QwikiWeb by subscribing to the RssFeed\n*You might also benefit from this ''[[general tutorial|http://www.blogjones.com/TiddlyWikiTutorial.html]]'' on TiddlyWiki
|!The following shows examples of special syntax to add formatting to your tiddlers:|\n\nWikiWord links:\nSimply use more than one captial letter and no spaces to make a word a tiddler reference.\n\nNon-WikiWord links:\nIf you want to reference a tiddler title that does not conform to the WikiWord format, simply surround it with brackets:\n[[Here is a sample of a Non-WikiWord link]]\n[[another]]\n\nStandard formatting:\n''Bold''\n==Strikeout==\n__Underline__\n//Italic//\n2^^3^^=8 (superscript)\na~~ij~~ = -a~~ji~~ (subscript)\n\nColor formating:\nNote: you can use hex color codes or color names for color formatting.\n@@highlight@@\n@@color(green):green colored@@\n@@bgcolor(#ff0000):red background@@\n\nEmbedded images:\n[img[Fractal vegetable|fractalveg.jpg]]\n\nExternal Links:\n[[Text that will be linked to a website|http://snipurl.com/qwikiweb]], or\n[[A link to another file on the same server|codediff.htm]]\n\nHorizontal Rules:\n----\n\nTables:\n|!table header cells are preceded with an exclamation point|regular cells are not|\n|>|<------ You can span multiple columns by using the "greater than" symbol ------>|\n|You can span multiple rows by using the "tilde" symbol|non-spanned row|\n|~|non-spanned row|\n|cells are left-aligned by default|''Note:'' //standard formatting syntax also works in table cells//|\n| add a space on the left of the text to right-align the text|~|\n| add spaces on both left and right to center cell text |~|\n|bgcolor(#d0d0d0):manually change the background color for a cell|~|\n\n*Bulleted lists\n*Bulleted lists\n**Bulleted lists\n***etc.\n\n#Numbered lists\n#Numbered lists\n##Numbered lists\n###etc.\n\n>Block quotes\n>Block quotes\n>>Block quotes\n>>>etc.\n\nHeadings:\n!Header 1\n!!Header 2\n!!!Header 3\n!!!!Header 4\n!!!!!Header 5\n\n{{{Inline monospaced text}}} or\n{{{\nMulti-line blocks of\nmonospaced text\n}}}
English default values are hardcoded into QwikiWeb (which means that you can delete this tiddler). But you can also customize these wordings by editing the following items. Enter your preferred text after the equals signs (no quotes are needed). Any blank or deleted items will revert back to the original hardcoded default. You can use HTML character codes (read SpecialCharacters) for tab, link, opt, cap, and txt items. For btn items, paste in the actual special character you wish to insert.\n\n|''Tab-related''|\n:tabTimeline=Timeline\n:tabTimelineTitle=Show all tiddlers by date\n:tabAll=All\n:tabAllTitle=Show all tiddlers in alphabetical order\n:tabTags=Tags\n:tabTagsTitle=Show tiddler category tags\n:capTagsNoneExist=There are no tagged tiddlers\n:tabMore=More\n:tabMoreTitle=Show other tiddler lists\n:optAll=All\n:capAll=All tiddlers in alphabetical order\n:optMissing=Missing\n:capMissing=Tiddlers that have links to them but are not defined\n:optOrphans=Orphans\n:capOrphans=Tiddlers that are not linked to from any other tiddlers\n:optSpecial=Special\n:capSpecial=Tiddlers that serve special purposes within QwikiWeb\n\n|''Tag-related''|\n:capNoTags=no tags\n:capTags=tags\n:capTagsTitle=Show tiddlers tagged with\n:capTagsNoOther=No other tiddlers tagged with\n\n|''Sidebar Commands''|\n:lnkSearch=search\n:lnkSearchTitle=Search this site for the word or phrase in the box below\n:lnkCloseAll=close all tiddlers\n:lnkCloseAllTitle=Close all displayed tiddlers (except any that are being edited)\n:lnkPermaview=permaview\n:lnkPermaviewTitle=Link to an URL that retrieves all the currently displayed tiddlers\n:lnkOptions=options\n:lnkOptionsTitle=Change TiddlyWiki interface options\n:lnkShowAdvanced=show advanced options\n:lnkShowAdvancedTitle=Turn advanced EditMode on\n:lnkHideAdvanced=hide advanced options\n:lnkHideAdvancedTitle=Turn advanced EditMode off\n\n|''Edit Comands''|\n:lnkCreateNew=• create new tiddler\n:lnkCreateNewTitle=Create a brand new tiddler\n:lnkSaveChanges=• save changes\n:lnkSaveChangesTitle=Save all tiddlers to create a new TiddlyWiki\n:lnkRestart=• restart tiddlers\n:lnkRestartTitle=Close all tiddlers and reopen the DefaultTiddlers (does not reload page)\n:lnkSiteSettings=• site settings\n:lnkSiteSettingsTitle=Configure the settings for this site\n:lnkInterfaceOptions=• interface options\n:lnkInterfaceOptionsTitle=Change TiddlyWiki interface options\n\n|''Toolbar Buttons''|\n:btnClose=close\n:btnCloseTitle=Close this tiddler\n:btnEdit=edit\n:btnEditTitle=Edit this tiddler\n:btnCollapse=collapse\n:btnCollapseTitle=Collapse this tiddler\n:btnExpand=expand\n:btnExpandTitle=Expand this tiddler\n:btnCloseOthers=close others\n:btnCloseOthersTitle=Close all tiddlers except this one\n:btnPermalink=permalink\n:btnPermalinkTitle=Permalink for this tiddler\n:btnReferences=references\n:btnReferencesTitle=Show tiddlers that link to this one\n:btnDone=done\n:btnDoneTitle=Save changes to this tiddler\n:btnCancel=cancel\n:btnCancelTitle=Undo changes to this tiddler\n:btnSpellCheck=spellcheck\n:btnSpellCheckTitle=Spellcheck this tiddler using SpellBound (you must first click in the tiddler's edit box)\n:btnDuplicate=duplicate\n:btnDuplicateTitle=Duplicate this tiddler\n:btnDelete=delete\n:btnDeleteTitle=Delete this tiddler\n:btnEditHelp=help\n:btnEditHelpTitle=Help on editing & formatting tiddlers\n\n|''InterfaceOptions''|\n|"tid..." items are WikiWords next to checkboxes. If you change the name here, ''be sure'' to change the respective tiddler's title for the link will to work.|\n|"txt..." items are pieces of text that combine to form the heading & username descriptions. ''Tip:'' Be sure to include leading/trailing spaces to separate words when compiled.|\n|"fld..." items are default values for form fields.|\n:txtHeading1=These \n:tidInterfaceOptions=InterfaceOptions \n:txtHeading2= for customizing \n:tidTiddlyWiki=TiddlyWiki \n:txtHeading3= are saved in your browser\n\n:txtUsername1=Your username for signing your edits. Write it as a \n:tidWikiWord=WikiWord \n:txtUsername2= (e.g. \n:tidJoeBloggs= JoeBloggs\n:txtUsername3=)\n:fldUsernameDefault=YourName\n\n:tidSaveBackups=SaveBackups\n:tidAutoSave=AutoSave\n:tidGenerateRss=GenerateAnRssFeed\n:tidSaveEmpty=SaveEmptyTemplate\n:tidShowHidden=ShowHiddenTiddlers\n:tidRegExpSearch=RegExpSearch\n:tidCaseSensitive=CaseSensitiveSearch\n:tidEnableAnimations=EnableAnimations\n\n|''Other Variables''|\n|Other customizable settings|\n:varDeleteSearchTrigger=DeleteAllContent\n:varDuplicateSuffix=Copy\n:varDefaultMainMenuText=MainMenu\n:varNumRssItems=20\n
|The following are the default values that are hardcoded into QwikiWeb (i.e. which means that you can delete this tiddler without affecting the default interface). To customize these wordings, simply make your edits after the equals signs. No quote marks are needed. And any items you delete or leave blank after the equals sign will revert back to the original default value that is hardcoded.|\n|''Syntax Notes:'' There should be four tilde ("~") characters at the very beginning of the first customized message, and each message thereafter should be separated by two tilde characters. Quotes are included to help show leading and trailing spaces, but are not required. If you want to embed a double quote mark, you need to preceed it with a "\s" character. Any included hard returns will appear in the final message display.|\n~~~~\n:popSaveTest="It appears that this TiddlyWiki has been incorrectly saved. Please see http://www.tiddlywiki.com/#DownloadSoftware for details"\n~~\n:popSaveWarning="You need to save this TiddlyWiki to a file before you can save changes"\n~~\n:popIncompatibleBrowserSave="It's not possible to save changes using this browser. Use FireFox if you can"\n~~\n:popInvalidTiddlyWiki1="The file "\n~~\n:popInvalidTiddlyWiki2=" doesn't appear to be a valid TiddlyWiki"\n~~\n:popErrorBackupSave="Couldn't save backup file"\n~~\n:popErrorRssSave="Failed to save RSS feed"\n~~\n:popErrorTemplateSave="Failed to save empty template file"\n~~\n:popErrorFileSave="Failed to save file"\n~~\n:popErrorDeleteAllContent="There was an error deleting the tiddler content."\n~~\n:popConfirmRssSaveAll="You have selected to GenerateAnRssFeed but have also made all hidden tiddlers visible. This will publish any hidden tiddlers to the RssFeed. Proceed with saving the RssFeed?"\n~~\n:popConfirmDeleteAll1="By searching for the phrase \s""\n~~\n:popConfirmDeleteAll2="\s" you have triggered the action to delete the contents of this site and start over with a blank TiddlyWiki.\nIf you really want to delete all the current tiddlers and start over, click OK/Yes.\nOtherwise click Cancel/No."\n~~\n:popConfirmDeleteAllSuccess="All tiddler content has been deleted. You can now enter new site title, subtitle, menu, etc. to start your new wiki.\nIf you did not want to delete the other content, you can still refresh the web page to return to the previously saved copy.\nWhen you are done, don't forget to use \s"save changes\s" to preserve your new site contents.\nDo you want to recreate the DeleteAllTiddlers instructions for future use?"\n~~\n:popMissingEditHelp="1The 'EditingHelp' tiddler is missing and cannot be displayed"\n~~\n:msgBackupSave="Backup file saved as"\n~~\n:msgRssSave="RSS feed saved as"\n~~\n:msgTemplateSave="Empty template saved as"\n~~\n:msgFileSave="Main file saved as"\n~~\n:msgMissingNewTiddler="This tiddler doesn't yet exist. If you are in advanced edit mode, you can double-click here to create it."
''Question:'' Why isn't QwikiWeb using the most recent TiddlyWiki codebase?\n----\n''Answer:''\nMost of the time, minor TiddlyWiki code updates can be incorporated into QwikiWeb quickly. However, when their are larger changes (such as was the case when "Tag support" was introduced), it takes longer. This is because QwikiWeb tries to keep its WebsiteOriented focus and its ease of use for beginning users who might be confused by newer, more advanced features. So the TiddlyWiki changes are incorporated into QwikiWeb carefully so as to not diminish the simple look and feel of the interface.\n\nRest assured that if TiddlyWiki has been updated, I'm working on porting those changes (in some form) into QwikiWeb.
''Question:'' Why can't I save my edits on my webserver?\n----\n''Answer:''\nQwikiWeb (and TiddlyWiki) are both designed as "stand-alone" wiki solutions. This means that you can edit and save changes to the file ''as long as the file is stored on your local computer''. You then upload that new wiki file to your webserver to allow others to see your new content.\n\nBut you can't ''save'' changes when viewing the webserver copy of your wiki unless you are using one of the special [[adaptations|http://www.tiddlywiki.com#TiddlyWikiAdaptations]] (like ZiddlyWiki or PHPTiddlyWiki) that is designed to work with a server-side script that handles saving changes.\n\nSo why doesn't QwikiWeb support a server-side script? Because, I wrote QwikiWeb aimed at users who want to create a website without learning HTML. This type of user most likely doesn't have server-configuration experience and may not even have access to a hosting server that allows them to run scripts on their website. So the stand-alone option seems best for them.
''Question:'' What should I do if I find a problem or bug with QwikiWeb?\n----\n''Answer:''\nYou should do the following:\n#Determine whether the problem is specific to QwikiWeb or whether it also shows up in TiddlyWiki (you may need to download a copy of TiddlyWiki from http://www.tiddlywiki.com and play around with it to see if you can duplicate the issue). Any problems that are evident in both QwikiWeb and TiddlyWiki should be reported to the author of TiddlyWiki, JeremyRuston (EmailMe).\n#Determine if the problem is specific to your computer or to your browser installation by trying to duplicate the problem on another machine that has the same browser. If you are using FireFox, you may also need to test disabling any extensions that you have which might be interfering with the way QwikiWeb works (for example, GreaseMonkey is notorious for causing problems in TiddlyWikis).\n#If you still think the problem is caused by QwikiWeb code, then send an email to AlanHecht (EmailMe).
QwikiWeb Frequently Asked Questions (QwikiWebFAQ)\n----\n|bgcolor(#d0d0d0): Click on the ''FAQ number'' to access the answer to the following questions:|\nFAQ001 - What should I do if I find a problem or bug with QwikiWeb?\nFAQ002 - Why can't I save my edits on my webserver?\nFAQ003 - Why isn't QwikiWeb using the most recent TiddlyWiki codebase?
''QwikiWeb revision highlights:''\nThe following modifications were added by AlanHecht and are illustrated in CodeDifference:\n----\n|bgcolor(#d0d0d0): Info on TiddlyWiki code changes can be found at http://www.tiddlywiki.com/#RevisionHistory |\n*''Version 1.2.22 [ach07k] [July 12, 2005]''\n**Added support for tags and for hiding tags using UserMode.\n**''Note:'' I recommend that you visit the [[extensions page|extenstions.htm]] for QwikiWeb-like plug-ins that work with TiddlyWiki 1.2.23 or higher.\n\n*''Version 1.2.20 [ach07j] [July 6, 2005]''\n**Fixed an error that would appear in FireFox when attempting to load the page. [Element referenced by ID/NAME in the global scope. Use W3C standard document.getElementById() instead. Line 233: searchText.focus();]\n\n*''Version 1.2.20 [ach07i] [June 24, 2005]''\n**Added an item in LingoMessages that sets the default text for a non-existing tiddler (i.e. "This tiddler does not exist. Double-click to create it.")\n\n*''Version 1.2.20 [ach07h] [June 23, 2005]''\n**Fixed a problem with the page displaying after using DeleteAllTiddlers\n\n*''Version 1.2.20 [ach07g] [June 20, 2005]''\n**Fixed a problem that would prevent the page from displaying if the LingoMessages tiddler was deleted\n\n*''Version 1.2.20 [ach07f] [June 16, 2005]''\n**Separated the text overlay settings (in LingoInterface) for the text that appears on mouse hover over the collapse and expand button so that they can each be different\n**Added a few extra items to customize for ColorThemes (notice: ColorThemes will change again in the next release thanks to [[a tip|http://shared.snapgrid.com/gtd-forum/viewtopic.php?t=71]] for getting past IE's CSS limitations. I had previously had to "dumb down" my themes so they would work with IE; now I can go back and redo them better.)\n**Added the option in LingoInterface to change the number of RSS items that get published\n**Fixed a problem that would prevent the page from displaying if the StickySettings tiddler was deleted\n\n*''Version 1.2.20 [ach07e] [June 15, 2005]''\n(//for more details read// ACH07)\n**ach07f revision: (June 16)\n***Incorporated JeremyRuston's changes in the 1.2.21 release\n***Separated the text overlay settings (in LingoInterface) for the text that appears on mouse hover over the collapse and expand button so that they can each be different\n***Added the option to change the number of RSS items published to LingoInterface\n**ach07e revision: (June 15)\n***Fixed a problem with UserMode and ColorThemes not being displayed properly\n***Added 2 missing elements (btnCloseOthers & btnCloseOthersTitle) to LingoInterface\n**ach07d revision: (June 15)\n***Incorporated JeremyRuston's changes in the 1.2.20 release\n***Fixed a problem with how the LanguageOverlay affected the editor's username setting\n**ach07c revision: (June 14)\n***Corrected some misleading text especially in the ColorTheme... tiddlers\n***Reworked my adjustments to the More tab's "Missing" links; previously some missing tiddlers were not showing up correctly or were showing up by accident.\n***Added ColorThemeCran and ColorThemeTeal predefined template samples\n***Other minor code changes & bug fixes\n**ach07b revision: (June 14)\n***Incorporated JeremyRuston's changes in the 1.2.19 release \n**ach07 revision: (June 13)\n**Incorporated JeremyRuston's changes in the 1.2.16-1.2.18 releases including the new StorageModel and the MoreTab\n**Tweaked the MoreTab so it is only visible while in EditMode (so it can be hidden from web visitors) and so that it responds to the status of HiddenTiddlers\n**Added a LanguageOverlay system which allows the wording for the entire QwikiWeb interface to be drawn from tiddlers. This also means that any language changes you make will survive an upgrade to the latest code version. The Language Overlay is broken down into two tiddler: LingoInterface and LingoMessages.\n**Added a new feature called UserMode that allows the author to select how complicated the interface is. There is one viewing mode for viewing the file online and one for viewing it locally. This feature replaces the previous LockEditMode & ForceEditMode which required external javascript files.\n**Added two new buttons to the tiddler toolbar: "collapse/expand" and "close others."\n**Added an option after using DeleteAllTiddlers to reinsert the directions tiddler for future use (since that feature is not documented elsewhere)\n**Optimized some of the original QwikiWeb code to enhance performance and decrease size. The newest code has not been optimized yet, but will be in the near future.\n*For earlier revision info, read OldRevisionHighlights
These options are called "StickySettings" because they only get loaded when the page is initially opened. This means that only someone who has editing rights and who can resave the page will be able to change StickySettings. Right now there is only one category of StickySettings (UserMode), but we can imagine more.\n----\n|>|UserMode|\n|>|The userModeWeb option sets the UserMode setting when viewing this page from a web server URL (http:). The userModeLocal option sets the UserMode setting when viewing this page from a local URL (file:). The UserMode settings currently have the following options (which are case sensitive):|\n||''standard'': (default mode) EditMode can be toggled on/off by showing or hiding the "advanced options." This gives access to the entire feature set while hiding things like the "save changes" command and each tiddler's "edit" button until they are needed. Editing tiddlers by double-clicking is also disabled if EditMode is off.|\n||''editor:'' Forces EditMode on. This is used mainly in userModeLocal to allow instant access to all of the editing functions.|\n||''readonly'': Locks EditMode so that the user cannot see any edit functions or the "show advanced" link that turns EditMode on.|\n||''simple'': Same as readonly, but also removes the following: permaview, close others, permalink, references, and the all interface options except for EnableAnimations (which is left to ensure browser compatibility)|\n||''bare'': Similar to readonly, but removes everything except the tiddler "close" button and the search command.|\n||''custom'': If you chose this mode, you can manually edit the "customMode()" function in this page's javascript to set up your own personalized set of viewer settings.|\n|>|''Additionally, you can add the phrases {{{+notabs}}} to the END of any the above modes to disable the sidebar tabs or tags for that mode setting.''|\n|>|''You can also add the phrases {{{+notags}}} to the END of any mode to hide any sign of tags.''|\n|>|''Note:'' The old format of {{{=notabs}}} will still work.|\n\n|>|//examples://|\n||{{{:userModeWeb=readonly+notabs}}}|\n||{{{:userModeWeb=readonly+notabs+notags}}}|\n||{{{:userModeLocal=editor}}}|\n|>|Now use the following lines to set your UserMode preferences.|\n:userModeWeb=standard\n:userModeLocal=standard+notags\n
QwikiWeb is an "adaptation" of TiddlyWiki, meaning that an entirely new code set was required in order to change the way TiddlyWiki worked. Beginning with TiddlyWiki version 1.2.23, developers can change the way TiddlyWiki works ''without'' the need for changing the entire code set. Instead, ''plug-ins'' can achieve essentially the same result without the need for a full-blown adaptation.\n\nSo QwikiWeb (as an adaptation) is no longer in development. The latest version of QwikiWeb (ACH07k) is based on TiddlyWiki 1.2.22 and includes support for tags. For a list of plug-ins for the newer versions of TiddlyWiki, please visit my [[extensions page|extensions.htm]].
Биоинформатика
Задания и результаты
http://kodomo.cmm.msu.ru/~golergka
[[Третий семестр]]
[[Первый семестр|http://kodomo.cmm.msu.ru/~golergka/term1/]]\n[[Второй семестр|http://kodomo.cmm.msu.ru/~golergka/term2/]]\n[[Третий семестр]]\n\n[[Обо мне]]
(Хотя на самом деле работа осуществлялась в GNU/Linux (дистрибутив Debian), если верить приглашению на входе.) Следующим образом выглядит скрипт, выполняющий задание:\n{{{\n#!/bin/sh\nls_test () {\n echo $1 >> ls.txt\n ls $1 >> ls.txt\n echo "" >> ls.txt\n}\ninfoseq sw:rs3_ecoli >> rs3_ecoli.info\ninfoseq -help >> infoseq.help\necho "" > ls.txt\nls_test \nls_test -m\nls_test -r\nls_test -1\nPS1=\st::\sW$\nchmod 755 $HOME/.bash_profile\necho "PS1=\st::\sW$" >> $HOME/.bash_profile\nchmod 555 $HOME/.bash_profile\n}}}
SiteTitle SiteSubtitle MainMenu DefaultTiddlers ConfigTiddlers SiteUrl ExplicitTiddlers HiddenTiddlers NoSearchTiddlers StyleSheet LingoInterface LingoMessages
Результат данного зачётного занятия лежит в указанной директории на сервере.\nК сожалению, создание ссылок на эти файлы приводит к неправильной обработке windows-системами компьютерного класса количества свободного места, так что от ссылок пришлось отказаться.
!Блок 1: Последовательности нуклеиновых кислот\n# [[Работа в командной строке Unix]]\n# [[Банк EMBL]]\n# [[Программы пакета BLAST для работы с нуклеотидными последовательностями]]\n# [[Поиск сходных нуклеотидных последовательной, не кодирующих белки]]\n# [[Аннотирование фрагмента генома Klebsiella pneumoniae (зачетное занятие)]]\n\n!Блок 2: Структуры нуклеиновых кислот\n# [[Работа в ChemSketch: построение фрагмента ДНК]]\n# [[Работа с RasMol и 3DNA: анализ структур A- и B-форм ДНК]]\n# [[Структура РНК]]\n# [[Белок-нуклеиновые контакты]]
Результатов выполнения задания является файл [[NA.sk2|http://kodomo.cmm.msu.ru/~golergka/term3/practice6/NA.sk2]].
! Сравнение разных записей в EMBL\nС помощью [[документа моего белка|http://www.expasy.org/uniprot/BTUF_ECOLI]] на сайте Expasy, я нашёл все ссылки на мой белок и заполнил следующую таблицу.\n|Идентификатор записи EMBL |Тип молекулы |Класс данных |Раздел EMBL |Дата создания документа |Описание |Длина|\n|U00096|геномная ДНК|стандартный|прокариоты|22.01.2006|E.Coli K12 MG1655, полный геном|4639675|\n|U70214|геномная ДНК|стандартный|прокариоты|22.9.1996|E.Coli хромосомы, 4-6 минут|123171|\n|D26562|геномная ДНК|стандартный|прокариоты|23.04.1994|Заменён AP009048 20.01.2006|1|\n|AP009048|геномная ДНК|стандартный|прокариоты|22.01.2006|данная запись не была выдана поиском, но я решил её включить, учитывая строку выше|4646332|\n!Сравнение описаний гена Escherichia coli в двух разных записях EMBL\n||I|II|\n|ID записи|u70214|u00096|\n|Начало гена в записи|8737|177662|\n|Конец гена в записи|9537|178462|\n|Направление гена|прямое|обратное|\n|Примечания|приведена автоматическая аннотация гена, белок ещё не идентифицирован (yadT_ECOLI)||\n!Знакомство с записью гена из эукариотического генома\nВот схема кодирующих участков моего гена, ABC50:\n{{{\n<--[1364733..1364779]--[1364275..1364370]-\n-[1363986..1364112]--[1363803..1363840)]-\n-[1363611..1363718]--[1362183..1362257]-\n-[1361670..1361783]--[1359001..1359123]-\n-[1358481..1358581]--[1358299..1358384]-\n-[1357858..1357997]--[1357623..1357771]-\n-[1356846..1356929]--[1356507..1356631]-\n-[1356198..1356310]--[1355884..1356055]-\n-[1355641..1355715]--[1355478..1355548]-\n-[1352476..1352508]--[1352222..1352390]-\n-[1351983..1352047]--[1351818..1351890]-\n-[1351495..1351661]--\n}}}\nВсего обнаружено 23 экзона.
!Создание индексов\nДля поиска по геномам холерного эмбриона, синегнойной палочки и бактерии Pasteurella multocida были созданы соответствующие индексные файлы с помощью следующих команд:\n{{{\nformatdb -i //home/export/samba/public/tmp/vc_genome.fasta -p F -n vc\nformatdb -i //home/export/samba/public/tmp/pa_genome.fasta -p F -n pa\nformatdb -i //home/export/samba/public/tmp/pm_genome.fasta -p F -n pm \n}}}\n!Поиск в неаннотированном геноме\nСледующей моей задачей являлось провести поиск в геномах этих организмов генов, похожих на кодирующиую последовательность моего белка. Т.к. мы имеем дело с белком, а поиск необходимо было провести в геноме, то я использовал программу tblastn, как и все мои разумные однокурсники.\nХотя, надо отметить, что один момент для меня остался невыясненным. Как эта программа может учитывать иногда происходящий при трансляции сдвиг рамки считывания? Насколько я понимаю, это явление не слишком частое, но имеющее место - однако ген, предусматривающий такой сдвиг, такой программой найти будет невозможно, даже если сходство с искомым белком будет очень большое и хорошее. \nВот выполненные мной команды:\n{{{\nblastall -p tblastn -d vc -i btuf.fasta -o vc.search\nblastall -p tblastn -d pa -i btuf.fasta -o pa.search\nblastall -p tblastn -d pm -i btuf.fasta -o pm.search\n}}}\n|Поиск гомологов btuf_Ecoli |Геном //Vibrio Chloreae//|Геном //Pseudomonas Aeruginosa//|Геном //Pasteurella Multocida//|\n|>|>|>|''Характеристика лучшей находки:''|\n|E-value находки|4*10^^-43^^|3*10^^-24^^|8*10^^-5^^|\n|координаты выравнивания(-ий)в записи генома|8560..9297|5711..4956|13569..13294|\n|AC соответствующей записи EMBL|AE004308|AE004821 (теперь AE004091)|AE006047|\n|Координаты CDS в записи EMBL (если они есть)|223..4686|||\n|AC UniProt в записи EMBL (если есть)|Q9KPJ1||Q9CPD1|\n|''Число находок с Е-value<0,01''|2|4|2|\n|>|>|>|Лучшие находки при поиске по трём геномам:|\n|E-value:|10^^-42^^|6*10^^-24^^|4*10^^-4^^|\n|>|>|>|Общее число находок с E-value большим 0,01 - 6.|\n\nВот выравнивания, соответствующий лучшим находкам.\n//Vibrio Chloreae//:\n{{{\n>embl|AE004308|AE004308 Vibrio cholerae O1 biovar eltor str. N16961\n chromosome I, section 216 of 251 of the complete\n chromosome.\n Length = 10126\n\n Score = 168 bits (426), Expect = 4e-43\n Identities = 94/246 (38%), Positives = 142/246 (57%), Gaps = 7/246 (2%)\n Frame = +1\n\nQuery: 23 APRVITLSPANTELAFAAGITP--VGVSSYSDYPPQAQKIEQVSTWQGMNLERIVALKPD 80\n A R+I+L+P TE+A+AAG+ V VS YSDYPPQA ++E+V+ Q +N+E+I+ LKPD\nSbjct: 8560 AERIISLAPHATEIAYAAGLGDKLVAVSEYSDYPPQALELERVANHQTINIEKILTLKPD 8739\n\nQuery: 81 LVIAWRGGNAERQVDQLASLGIVMWVDAT-SIEQIANALRQLAPWSPQPDKAEQAAQSLL 139\n L+IAW GN R++ +L LG ++ T ++++IA+ + L+ +S P+ ++AA \nSbjct: 8740 LIIAWPAGNPPRELAKLRQLGFTIYDSQTKTLDEIADNIEALSHYSANPEVGQKAAHDFR 8919\n\nQuery: 140 DQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKDSRVPWPQVS 199\n + L+ QYA R F Q P T + ++V +CGG NIF DS VP+PQVS\nSbjct: 8920 QRLQDLRTQYASNQPIRYFYQLSEKPIITLAQGHWPSEVFSLCGGVNIFADSEVPYPQVS 9099\n\nQuery: 200 REQVLARSPQAIVITGGPDQIPKIKQYWGEQLKI----PVIPLTSDWFERASPRIILAAQ 255\n EQVL + PQ I + + + W +L V L +DW R +PR + A +\nSbjct: 9100 IEQVLVKQPQVIFTSEHAIANGHMWRAWQAELSAVQNDQVWALNADWLNRPTPRTLDAVE 9279\n\nQuery: 256 QLCNAL 261\n Q+C L\nSbjct: 9280 QVCTYL 9297\n}}}\n//Pseudomonas Aeruginosa//:\n{{{\n>embl|AE004821|AE004821 Pseudomonas aeruginosa PAO1, section 382 of\n 529 of the complete genome.\n Length = 10842\n\n Score = 106 bits (265), Expect = 3e-24\n Identities = 77/254 (30%), Positives = 128/254 (50%), Gaps = 6/254 (2%)\n Frame = -2\n\nQuery: 15 LAPLWLNAAPRVITLSPANTE--LAFAAGITPVGVSSYSDYPPQAQKIEQVSTWQGMNLE 72\n L L AA RV++L+P+ T+ L A VGV + P + V + +NLE\nSbjct: 5711 LLSLSAGAAQRVVSLAPSLTDSVLELGAARRLVGVLDGGERPAAIGDLPSVGRYGQVNLE 5532\n\nQuery: 73 RIVALKPDLVIAWRGGNAERQVDQLASLGIVMWV-DATSIEQIANALRQLAPWSPQPDKA 131\n R++ L+PDL++ W G E Q+ +L GI +++ + S++++A L L + + \nSbjct: 5531 RLLELQPDLILVWPGSVPEAQLQRLRDFGIALFIAEPHSLDELALQLAALGEALGEAEAG 5352\n\nQuery: 132 EQAAQSLLDQYAQLKAQYA-DKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKD 190\n ++ + + +L +Y DKP K VF Q P +T G + + L VCG EN+F D\nSbjct: 5351 QRLSARFREGMRRLAERYRRDKPLK-VFYQVWDRPLYTIGGRQVISDALRVCGAENLFGD 5175\n\nQuery: 191 SRVPWPQVSREQVLARSPQAIVITGGPDQIPKIKQY--WGEQLKIPVIPLTSDWFERASP 248\n P PQVS E VLAR P A+++ G Q+ +Q+ + + + ER S \nSbjct: 5174 LPQPAPQVSVEAVLARDP-AVIVAGSHAQLELWRQWPALAATRRGQLYRIEDKNLERPSF 4998\n\nQuery: 249 RIILAAQQLCNALS 262\n ++ A ++LC +L+\nSbjct: 4997 AMLAATEKLCRSLA 4956\n}}}\n//Pasteurella Multocida//:\n{{{\n>embl|AE006047|AE006047 Pasteurella multocida subsp. multocida str. Pm70\n section 14 of 204 of the complete genome.\n Length = 13792\n\n Score = 40.8 bits (94), Expect = 8e-05\n Identities = 29/92 (31%), Positives = 46/92 (50%), Gaps = 8/92 (8%)\n Frame = -2\n\nQuery: 1 MAKSLFRALVALSFLAPLWLNAAP-RVITLSPANTELAFAAGITPVGVSSYSDYPPQAQK 59\n MA A+ L++ P RV+ L + + G++PVGV+ +D QK\nSbjct: 13569 MASQFVSAVTVKDQKGEFTLDSVPKRVVALEYSYVDALAQIGVSPVGVADDNDKTRILQK 13390\n\nQuery: 60 I-EQVSTWQGM------NLERIVALKPDLVIA 84\n + ++V W+ + +LE I ALKPDL+IA\nSbjct: 13389 VRDKVQPWESVGTRSQPSLEAISALKPDLIIA 13294\n}}}\nК сожалению, из-за недоступности из моей домашней сети сервера SRS я не смог выполнить часть задания, касающуюся поиска информации о данных записях в БД EMBL.\n!Поиск гомологов с помощью blastn\nПоиск с помощью blastn был произведён с помощью следующей команды:\n{{{\nblastall -p blastn -d pm -i btuf.genome.fasta -o blastn.search\n}}}\nНо он дал весьма скудные результаты, и E-value лучшей находки оказался равен 0,36.\nВот выравнивание, ей соответствующее:\n{{{\nQuery: 560 acatctttaaagacag 575\n ||||||||||||||||\nSbjct: 445 acatctttaaagacag 460\n}}}
<<<\nВаша задача — выбрать тРНК у кишечной палочки (Escherichia coli K-12) и найти наиболее похожую на нее последовательность в родственном геноме. В качестве "родственного" генома мы предлагаем вам геном достаточно далекого организма – геном сенной палочки (Bacillus subtilis), см. P:/tmp/bs_genome.fasta \n<<<\n!Определите, какая тРНК была использована рибосомой при присоединении 4-ого аминокислотного остатка к растущей цепи Вашего белка\n<<<\n\n<<<\nБыл произведён поиск по файлу [[ecoli.embl|http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&qty=1&c_start=1&list_uids=U00096&uids=&dopt=gbwithparts&dispmax=5&sendto=t&fmt_mask=0&truncate=294912&from=begin&to=end&extrafeatpresent=1&ef_tRNA=128]] с помощью команды\n{{{\n$ grep -in serine ecoli.tRNA.embl | grep -i trna\n}}}\n, реультат выполнения которой приведён ниже:\n{{{\n20322: serine tRNA5;\n20570: /note="serine tRNA synthetase; also charges selenocystein\n20571: tRNA with serine"\n20575: selenocysteinyl-tRNA with serine"\n22373: serine tRNA1;\n23768: serine tRNA5;\n45177: serine tRNA2;\n61821: serine tRNA3;\n}}}\nТаким образом, в геноме //E. Coli// закодировано 4 тРНК для серина.\nКодон, соответствующий моему, узнаёт ''tRNA1''.\n|>|Аминокислотный остаток в 4-ой позиции белка btuf_ecoli|''S''|\n|>|Соответствующий кодон в гене btuf|5'-''tc__a__''-3'|\n|>|Соответствующий кодон в мРНК|5'-''uc__a__''-3'|\n|>|Идеальный антикодон |5'-''__u__ga''-3'|\n|>|Сколько можно было бы ожидать разных тРНК для остатка ''S'', если опираться на генетический код? |''6''|\n|>|Сколько разных тРНК для остатка ''S'' аннотировано в геноме кишечной палочки?|''4''|\n|>|>| Характеристика выбранной для дальнейшего изучения тРНК: |\n||имя гена|''serT''|\n||локализация гена в геноме|''925107..925194'', комплементарная цепь|\n||распознаваемый кодон|''ucd''|\n||антикодон|''uga''|\nПоследовательность этой РНК:\n{{{\nGGAAGTGTGGCCGAGCGGTTGAAGGCACCGGTCTTGAAAACCGGCGACCCGAAAGGGTTCCAGAGTTCGAATCTCTGCGCTTCCGCCA\n}}}\n!Поиск гомологичных тРНК в родственном геноме\nК сожадению, поиск с помощью ''fasta34'' не удался. Вот вывод программы:\n{{{\n$ cat tRNA.fasta\nGGAAGTGTGGCCGAGCGGTTGAAGGCACCGGTCTTGAAAACCGGCGACCCGAAAGGGTTCCAGAGTTCGAATCTCTGCGCTTCCGCCA\ngolergka@golergka-desktop:~/bioinf$ fasta34 tRNA.fasta bs_genome.fasta\n# fasta34 tRNA.fasta bs_genome.fasta\nFASTA searches a protein or DNA sequence data bank\n version 3.4t26 July 7, 2006\nPlease cite:\n W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448\n\n\n***[fasta34] Query sequence length <= 0: tRNA.fasta***\n}}}\nЯ не имею представления, чем вызвана эта ошибка, т.к. в файле tRNA.fasta хранится полная последовательность тРНК в том виде, в котором я привёл её выше.\n|>|''Программа''|''FASTA''|''BLASTN''|''MegaBLAST''|''discontiguous MegaBLAST''|\n|>|Длина якоря| | | | |\n|>|Результаты поиска| |[[bln_trna.search|http://kodomo.cmm.msu.ru/~golergka/term3/practice4/bln_trna.search]] |[[mblast_trna.search|http://kodomo.cmm.msu.ru/~golergka/term3/practice4/mblast_trna.search]] |[[dcmblast_trna.search|http://kodomo.cmm.msu.ru/~golergka/term3/practice4/dcmblast_trna.search]] |\n|>|Число находок с E-value < 0,01| |0 |0 |0 |\n|>|Характеристика лучшей находки:| | | | |\n||E-value| |0,063 |хитов нет |0,063 |\n||длина выравнивания| |24 | |24 |\n||вес выравнивания| |32 | |32 |\n||координаты в геноме| |158354..158331 | |158354..158331 |\n|>|Аннотация лучшей находки по записи EMBL:| | | | |\n||имя гена| | | | |\n||это тРНК?| | | | |\n|| | | | | | \nК сожалению, из-за проблем с работой с сервером srs.ebi.co.uk я не смог найти аннотацию к этим записям.\n\nНиже приведены соответственные выравнивания.\n''BLASTN'':\n{{{\n>Z99119 Z99119 Bacillus subtilis complete genome (section 16 of 21): from\n 3013458 to 3213379.\n Length = 199922\n\n Score = 32.2 bits (16), Expect = 0.063\n Identities = 22/24 (91%)\n Strand = Plus / Minus\n\n \nQuery: 20 tgaaggcaccggtcttgaaaaccg 43\n |||||| | |||||||||||||||\nSbjct: 158354 tgaagggatcggtcttgaaaaccg 158331\n}}}\n''discontiguous MegaBLAST'':\n{{{\n>Z99119 Z99119 Bacillus subtilis complete genome (section 16 of 21): from\n 3013458 to 3213379.\n Length = 199922\n\n Score = 32.2 bits (16), Expect = 0.063\n Identities = 22/24 (91%)\n Strand = Plus / Minus\n\n \nQuery: 20 tgaaggcaccggtcttgaaaaccg 43\n |||||| | |||||||||||||||\nSbjct: 158354 tgaagggatcggtcttgaaaaccg 158331\n}}}\n\nВ итоге можно с уверенностью сказать, что это полный гомолог указанной тРНК.
Необходимые файлы были получены следующим путём:\n{{{\n$ fiber -a gatc-a.pdb\nFiber data in directory: /home/golergka/X3DNA/FIBER/\nStructure #1; Twist: 32.7 (degrees); Rise: 2.548 (Angstrom)\n\nInput your base sequence with only A,C,G & T:\n1. From a data file (complete sequence)\n2. From keyboard (enter only the repeating sequence)\nYour choice (1 or 2, Dft: 2): 2\n\nRepeating unit (Dft: polyA): gatc\nRepeating unit: GATC\nNumber of repeats (Dft: 10): 4\n$ fiber -a gatc-a.pdb\nFiber data in directory: /home/golergka/X3DNA/FIBER/\nStructure #1; Twist: 32.7 (degrees); Rise: 2.548 (Angstrom)\n\nInput your base sequence with only A,C,G & T:\n1. From a data file (complete sequence)\n2. From keyboard (enter only the repeating sequence)\nYour choice (1 or 2, Dft: 2): 2\n\nRepeating unit (Dft: polyA): gatc\nRepeating unit: GATC\nNumber of repeats (Dft: 10): 4\n}}}\nВот они: [[gatc-a.pdb|http://kodomo.cmm.msu.ru/~golergka/term3/practice7/gatc-a.pdb]], [[gatc-b.pdb|http://kodomo.cmm.msu.ru/~golergka/term3/practice7/gatc-b.pdb]].\nБыла заполнена следующая таблица:\n||A-форма|B-форма|dna54.pdb|\n|Тип спирали (правая или левая)|правая|правая||\n|Шаг спирали (Å)|28.02|33.75|27.07|\n|Число оснований на виток|11|10|12|\n|Ширина большой бороздки|7.9|17|17|\n|Ширина малой бороздки|16.8|11.6|10.5|\nШирины бороздок даны в среднем.\n\nБыл произведён анализ pdb-файлов с помощью команд типа:\n{{{\nfind_pair -t gatc-a.pdb stdout | analyze && find_pair -t gatc-b.pdb stdout | analyze && find_pair -t dna54.pdb stdout | analyze\n}}}\nполучены следующие файлы: [[gatc-a.out|http://kodomo.cmm.msu.ru/~golergka/term3/practice7/gatc-a.out]], [[gatc-b.out|http://kodomo.cmm.msu.ru/~golergka/term3/practice7/gatc-b.out]], [[dna54.out|http://kodomo.cmm.msu.ru/~golergka/term3/practice7/dna54.out]].\n||α |β |γ |δ |ε |ζ |χ |\n|A|-51,7|174,8|41,7|79,1|-147,8|-75,1|-157,2|\n|B|-29,9|136,3|31,2|143,3|-140,8|-160,5|-98,0|\n|dna54||||||||\n{{{\nNote: alpha: O3'(i-1)-P-O5'-C5'\n beta: P-O5'-C5'-C4'\n gamma: O5'-C5'-C4'-C3'\n delta: C5'-C4'-C3'-O3'\n epsilon: C4'-C3'-O3'-P(i+1)\n zeta: C3'-O3'-P(i+1)-O5'(i+1)\n\n chi for pyrimidines(Y): O4'-C1'-N1-C2\n chi for purines(R): O4'-C1'-N9-C4\n\n}}}\nМой файл:\n{{{\n base alpha beta gamma delta epsilon zeta chi\n 1 U --- --- 64.9 84.7 -158.4 -73.3 -160.3\n 2 A -62.6 172.8 51.5 84.7 -152.5 -79.7 -166.0\n 3 C -59.3 167.3 53.4 86.9 -147.7 -82.4 -162.5\n 4 U -59.3 163.3 57.7 91.8 --- --- -155.3\n 5 A --- 153.1 -173.2 83.5 -170.0 -84.0 -147.7\n 6 C 158.8 -159.1 164.9 83.0 -114.8 -77.7 -151.1\n 7 G -57.7 145.5 71.1 74.8 -146.9 -85.1 -177.0\n 8 U -48.1 172.6 39.9 78.5 -147.7 -70.4 -161.2\n 9 A -57.7 170.0 47.9 79.7 -142.8 -79.2 -162.8\n 10 G -65.3 156.6 62.6 80.5 -146.4 -75.5 -170.0\n 11 U -62.6 168.4 54.8 81.8 -153.0 -73.7 -164.6\n 12 A -65.2 179.0 50.1 76.1 --- --- -157.0\n}}}\n\nТакже созданы были требуемые изображения всех трёх цепей ДНК с помощью программы ''pdb2img''.\n\nФорма A, вид сверху:\n[img[http://kodomo.cmm.msu.ru/~golergka/term3/practice7/a.png]]\nВид сбоку:\n[img[http://kodomo.cmm.msu.ru/~golergka/term3/practice7/a_r.png]]\nФорма B, вид сверху:\n[img[http://kodomo.cmm.msu.ru/~golergka/term3/practice7/b.png]]\nВид сбоку:\n[img[http://kodomo.cmm.msu.ru/~golergka/term3/practice7/b_r.png]]\nМой файл, вид сверху:\n[img[http://kodomo.cmm.msu.ru/~golergka/term3/practice7/dna54.png]]\nВид сбоку:\n[img[http://kodomo.cmm.msu.ru/~golergka/term3/practice7/dna54_r.png]]
Мною был скачан файл [[1ehz.pdb|http://www.rcsb.org/pdb/files/1ehz.pdb]]. Это структура фенилаланиновой тРНК из дрожжей.\nПривожу нуклеотидную последовательность этой тРНК:\n\nGCGGAUUUA''G''CUCAG''UU''GGGAGAGC''G''CCAGA''C''UG''A''AGA''U''CU''G''GAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA\n\n