Origin: Unknown -- Help Page

Origin: UnknownÓ Help

Introduction
Game Play Screens and Controls
Hardware and Software Considerations
Introduction
1. Purpose
  Origin: Unknown is intended to provide a fun avenue to supplement the teaching and learning of the use of WWW-based Bioinformatics tools in the analysis of biological macro-molecular sequence data.
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2. General Features of the Game
  During the game, the player is presented with a series of screens or pages which:
  1. Allow input of player name as well as selection of skill level and scenario
  2. Inform the player of the discovery of a sample of unknown origin
  3. Enable the player to analyze the sample for chemical content, to perform a sequence analysis on any DNA or protein sequences in the sample, and to utilize an array of Bioinformatics tools on the determined sequences
  4. Enable the player to record quantitative conclusions into a lab notebook
  5. Provide a performance indicator of the player’s conclusions
  6. Allow the submission of a final conclusion concerning the origin of the sample
  7. Present the player’s score (on a scale of 50,000) based on the conclusions made and the steps taken to reach the final conclusion.
  Various links throughout the game are provided for access to an online procedure manual that contains descriptions of scoring, game strategies, and the Bioinformatics tools used in the game. It also provides interactive tutorials for each Bioinformatics tool. Accessing this manual on game levels three and four will result in scoring penalties. This feature has been included to discourage skilled players from accessing the guide.
  News reports and commentary from the player's lab supervisor are provided as the game progresses.
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3. Basic Game Procedure and Strategy
  Upon receiving a sample, the player should request a chemical analysis to determine whether or not the sample contains DNA, protein, or both. If the chemical analysis does not reveal the presence of DNA and/or protein, there is no need to perform additional analysis; the player can proceed to the lab supervisor to make a final conclusion. If the analysis indicates the presence of DNA or protein, the sample should be sent out for sequence analysis. The player should then select the proper Bioinformatics tool(s) in order to continue analysis of the sample sequence(s). Based on the results obtained from using these tools, the player is to record his / her observations in the Lab Notebook by choosing from a set of possible observations. Finally, the player should report to the lab supervisor to submit a final conclusion regarding the origin of the sample. If the final conclusion was correct, the player will then receive a final report that displays the final score, conclusions to the game scenario, and a table comparing the optimal sequence of Bioinformatics tools to the sequence of tools that the player used in the scenario. If the final conclusion was incorrect or if the appropriate , the player will be fired for poor performance, but will have the opportunity to replay the same scenario.
  During game play, various penalties can be deducted from a starting score of 50,000. Action penalties are assessed for player activities (such as checking the procedure manual in upper difficulty levels). Procedure penalties are imposed if the player misinterprets Bioinformatics tool results, uses these tools unnecessarily, or attempts to make a conclusion without utilizing the proper tests or tools.
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Game Play Screens and Controls
1. Entry Screen
  1. Supporting Information - This includes a brief summary of the game, system requirements, and a disclaimer.
  2. Name entry - The player should provide his / her name in the appropriate entry box on the check-in screen. If no name is provided a default name is selected by the game based upon the chosen skill level.
  3. Game entry - A pull-down menu of the different scenarios, classified by difficulty level, is provided. To obtain a random scenario, a player can select either "Level" or "Random" under a particular level (no difference).
  4. Play! Button - Clicking will begin the game with the selected scenario.
  5. Procedure Manual link - A link to the procedure manual with its information and tutorials.
  6. Help link - A link to this help page
  7. View Credits link - A link to a description of the SWBIC Origin: UnknownÓ team and other key players in the production of the game.
  8. FAQ link - A link to a list of Frequently Asked Questions about Origin: UnknownÓ.
  9. SWBIC link - A link to SWBIC’s homepage
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2. Introduction Screen
  1. Media Report - Introduces the story line of the scenario and describes the details of the sample’s discovery.
  2. Assignment - The player’s assignment straight from the lab supervisor.
  3. Begin link - Clicking this link takes the player to the Space Laboratory to begin game play.
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3. Space Laboratory
  1. Chemical Analysis - A link to the Chemical Analysis Screen for analysis of the composition of the sample.
  2. Sequencing Tools - A link to the Sequence Analysis Screen for the sequencing of DNA or proteins in the sample.
  3. Computer Tools - A link to the Computer Home Screen for selection of subsequent game steps.
  4. Holo-Supervisor - A link to the Supervisor Screen for final game conclusions.
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4. Chemical Analysis Screen
  1. Yes / No buttons - Selecting yes will direct the game to perform a chemical composition analysis on the sample, but selecting no will return the player to the Space Laboratory.
  2. Sample Contents - Once a chemical analysis is performed, the results are displayed on the screen.
  3. Continue button - Clicking the continue button will record the chemical analysis results in the players game notebook and display the media update screen.
  4. Procedure Manual link - Clicking the link to the procedure manual will allow the player access to the information and tutorials contained in the manual. Remember that access to the procedure manual will cause a score deduction in levels 3 and 4.
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5. Media Update Screen
  1. News Report - The latest publicly released developments regarding the scenario.
  2. Supervisor Memo - Email contact from the lab supervisor, often in response to the media report
  3. Continue button - Clicking the continue button will return the player to the Space Laboratory.
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6. Sequence Analysis Screen
  1. Yes / No buttons - Selecting yes will direct the game to perform a sequence analysis on the DNA and/or protein in the sample, but selecting no will return the player to the Space Laboratory.
  2. DNA Sequence Analysis Results - Once a DNA sequence analysis is performed, the results are displayed on the screen.
  3. Protein Sequence Analysis Results - Once a protein sequence analysis is performed, the results are displayed on the screen.
  4. Continue button - Clicking the continue button will record the sequence analysis results in the players game notebook and display the media update screen.
  5. Procedure Manual link - Clicking the link to the procedure manual will allow the player access to the information and tutorials contained in the manual. Remember that access to the procedure manual will cause a score deduction in levels 3 and 4.
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7. Computer Home Screen
  1. Help Page Link - A link to this page.
  2. Bioinformatics Tools Link - A link to the Bioinformatics Tools Screen.
  3. Procedure Manual Link - A link to the Procedure Manual (there is a point penalty if the player is above difficulty level 2).
  4. Lab Notebook Link - A link to the Lab Notebook Table of Contents.
  5. Space Laboratory Link - A link back to the Space Laboratory.
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8. Supervisor Screen
  1. Final Game Conclusions - Allows the player to pick one of four final game conclusions.
  2. Submit Final Conclusion button - Submits the players final game conclusion for scoring and ends the game.
  3. Space Laboratory link - A link back to the Space Laboratory for the situation in which the player decides not to make a final conclusion.
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9. Bioinformatics Tools Screen
  According to the difficulty level, the player may choose from the following tools (for more detail and explanation of each tool, see the Procedure Manual):
  1. BLAST (All levels)
  2. NORF (Level 4)
  3. ClustalW (Level 3 and 4)
  4. BLOCKs (Level 3 and 4)
  5. Profile Scan (Level 4)
  6. Procedure Manual link - A link to the Procedure Manual (there is a point penalty if the player is above difficulty level 2).
  7. Space Laboratory link - A link back to the Space Laboratory.
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10. Lab Notebook Table of Contents
  The exact links available on this page during a game will differ depending on the difficulty level and scenario chosen by the player. The following descriptions cover all possible links.
  1. Sequences for Tool Input
    1. Sequence Analysis Results - A record of the results of the sequence analysis.
    2. NORF Results - A record of the results from a NORF analysis of sample DNA.
    3. Reformatted Sequences for ClustalW Input (levels 3 and 4 only) - When sequences are selected on the BLAST notebook pages to be reformatted for ClustalW analysis, those sequences are printed here. They may be copied for input into the ClustalW tool input page.
  2. ORF Info (level 4 only)
    1. BLAST Results for ORF
      Here, the player may enter conclusions based on the blastp results from performing BLAST on any identified ORFs. More detailed instructions on the selection of specific conclusions for BLAST may be found in the BLAST tutorial in the Procedure Manual. There may be more than one page here if more than one ORF has been identified.
      1. Submit Conclusions button - Clicking submits the selected conclusions to the game.
      2. Notebook Table of Contents link - A link back to the Lab Notebook. Table of Contents.
      3. Space Laboratory link - A link back to the Space Laboratory.
  3. Notebook Conclusions Pages for Tool Results
    1. Sample Composition Analysis Page - A record of the results of the composition of the sample.
    2. BLAST Results for Sample DNA Analyzed with blastn
      Here, the player may enter conclusions based on the blastn results. Each conclusion may be entered by clicking on the box or button by that conclusion. More detailed instructions on the selection of specific conclusions for BLAST may be found in the BLAST tutorial in the Procedure Manual.
      1. Submit Conclusions button - Clicking submits the selected conclusions to the game.
      2. Notebook Table of Contents link - A link back to the Lab Notebook. Table of Contents.
      3. Space Laboratory link - A link back to the Space Laboratory.
    3. BLAST Results for Sample Protein Analyzed with blastp
      Here, the player may enter conclusions based on the blastp results. Each conclusion may be entered by clicking on the box or button by that conclusion. More detailed instructions on the selection of specific conclusions for BLAST may be found in the BLAST tutorial in the Procedure Manual.
      1. Submit Conclusions button - Clicking submits the selected conclusions to the game.
      2. Notebook Table of Contents link - - A link back to the Lab Notebook.
      3. Space Laboratory link - A link back to the Space Laboratory.
    4. ClustalW Results for Sample DNA (levels 3 and 4 only)
      Here, the player may enter conclusions based on the ClustalW for DNA results. Each conclusion may be entered by clicking on the box or button by that conclusion. More detailed instructions on the selection of specific conclusions for ClustalW may be found in the ClustalW tutorial in the Procedure Manual.
      1. Submit Conclusions button - Clicking submits the selected conclusions to the game.
      2. Notebook Table of Contents link - - A link back to the Lab Notebook.
      3. Space Laboratory link - A link back to the Space Laboratory.
    5. ClustalW Results for Sample Protein (levels 3 and 4 only) Here, the player may enter conclusions based on the ClustalW for protein results. Each conclusion may be entered by clicking on the box or button by that conclusion. More detailed instructions on the selection of specific conclusions for ClustalW may be found in the ClustalW tutorial in the Procedure Manual.
      1. Submit Conclusions button - Clicking submits the selected conclusions to the game.
      2. Notebook Table of Contents link - - A link back to the Lab Notebook.
      3. Space Laboratory link - A link back to the Space Laboratory.
    6. ClustalW Results for best ORF found with NORF/BLAST (levels 3 and 4 only) Here, the player may enter conclusions based on the ClustalW for protein results. Each conclusion may be entered by clicking on the box or button by that conclusion. More detailed instructions on the selection of specific conclusions for ClustalW may be found in the ClustalW tutorial in the Procedure Manual.
      1. Submit Conclusions button - Clicking submits the selected conclusions to the game.
      2. Notebook Table of Contents link - - A link back to the Lab Notebook.
      3. Space Laboratory link - A link back to the Space Laboratory.
    7. BLOCKs Results for Sample DNA (levels 3 and 4 only)
      Here, the player may enter conclusions based on the BLOCKs for DNA results. Each conclusion may be entered by clicking on the box or button by that conclusion. More detailed instructions on the selection of specific conclusions for BLOCKs may be found in the BLOCKs tutorial in the Procedure Manual.
      1. Submit Conclusions button - Clicking submits the selected conclusions to the game.
      2. Notebook Table of Contents link - - A link back to the Lab Notebook.
      3. Space Laboratory link - A link back to the Space Laboratory.
    8. BLOCKs Results for Sample Protein (levels 3 and 4 only)
      Here, the player may enter conclusions based on the BLOCKs for protein results. Each conclusion may be entered by clicking on the box or button by that conclusion. More detailed instructions on the selection of specific conclusions for BLOCKs may be found in the BLOCKs tutorial in the Procedure Manual.
      1. Submit Conclusions button - Clicking submits the selected conclusions to the game.
      2. Notebook Table of Contents link - - A link back to the Lab Notebook.
      3. Space Laboratory link - A link back to the Space Laboratory.
    9. BLOCKs Results for best ORF found with NORF/BLAST (levels 3 and 4 only)
      Here, the player may enter conclusions based on the BLOCKs for ORF results. Each conclusion may be entered by clicking on the box or button by that conclusion. More detailed instructions on the selection of specific conclusions for BLOCKs may be found in the BLOCKs tutorial in the Procedure Manual.
      1. Submit Conclusions button - Clicking submits the selected conclusions to the game.
      2. Notebook Table of Contents link - - A link back to the Lab Notebook.
      3. Space Laboratory link - A link back to the Space Laboratory.
    10. ProfileScan Results for Sample Protein (levels 3 and 4 only)
      Here, the player may enter conclusions based on the ProfileScan for protein results. Each conclusion may be entered by clicking on the box or button by that conclusion. More detailed instructions on the selection of specific conclusions for ProfileScan may be found in the ProfileScan tutorial in the Procedure Manual.
      1. Submit Conclusions button - Clicking submits the selected conclusions to the game.
      2. Notebook Table of Contents link - - A link back to the Lab Notebook.
      3. Space Laboratory link - A link back to the Space Laboratory.
    11. ProfileScan Results for best ORF found with NORF/BLAST (levels 3 and 4 only)
      Here, the player may enter conclusions based on the ProfileScan for ORF results. Each conclusion may be entered by clicking on the box or button by that conclusion. More detailed instructions on the selection of specific conclusions for ProfileScan may be found in the ProfileScan tutorial in the Procedure Manual.
      1. Submit Conclusions button - Clicking submits the selected conclusions to the game.
      2. Notebook Table of Contents link - - A link back to the Lab Notebook.
      3. Space Laboratory link - A link back to the Space Laboratory.
  4. Space Laboratory link - A link back to the Space Laboratory.
  5. Procedure Manual link - A link to the Procedure Manual (there is a point penalty if the player is above difficulty level 2).
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11. Notebook Conclusions Confirmation Page
  This confirmation page provides the player with an indication of how well his / her conclusions match the proper conclusions for the tools results that have just been entered into the notebook. This is done with a red/yellow/green light indicator. (For more detail on the indicator, see the Procedure Manual.) If the indicator light is not green, the player is allowed to redo the notebook conclusions page or the tool analysis. If the player is satisfied with the indicator light he / she may confirm the results and continue the game. The chosen conclusions are displayed on this screen for player reference.
  1. Reinterpret Results button - Clicking will return the player to the notebook tool conclusions page that was just submitted and allow the player to change conclusions and resubmit them.
  2. Redo Tool Analysis button - Clicking will take the player to the computer screen and allow him / her to repeat the tool analysis.
  3. Confirm Results button - Clicking will confirm the players conclusions in the notebook and take them to a Media / Supervisor update screen.
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12. Game Results Screens
  1. Epilogue Page - This page is displayed only if the player's final conclusion was correct.
    1. Score - Display of the player's final score (out of 50,000 points).
    2. Sample Composition - A restatement of the sample's content.
    3. Epilogue - This is final information to conclude the scenario.
    4. Procedure Table (Your Game vs. Optimal) - This table shows the sequence of Bioinformatics tools that the player used to derive his / her final conclusion as compared to the optimal sequence of tools needed.
    5. Yes / No buttons - If the player’s final conclusion was correct, he / she may choose Yes to play the game again or No to return to the SWBIC home page.
  2. Fired Page - This page is displayed if the player's final conclusion was incorrect, or if the player has attempted to make a final conclusion without performing enough Bioinformatic tool analysis to make an attempt at a final conclusion.
    1. Yes / No buttons - If the player is fired, he / she may choose Yes to play the same scenario over again or No to return to the SWBIC home page.
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Hardware and Software Considerations
1. Platform - Origin: Unknown is platform independent. It has been tested on Windows 95, Linux, and FreeBSD PC's and MacIntosh's.
2. Browser - Origin: UnknownÓ is best viewed with Netscape version 4.X or later, Netscape Communicator, Internet Explorer 5.X or later, or other graphics and JAVA capable browsers.
3. Monitor and Display Settings - Origin: UnknownÓ is a very graphics intense game. Unfortunately there may be differences in the colors seen depending on the player's monitor. For the best possible color for Origin: UnknownÓ, the monitor should be set to a minimum of 64K colors.
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Please send comments and suggestions to: webmaste@swbic.org