Scorpion Manual V1.docx - Old Dominion University
Contents
1. Cancel N Developers Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu at This work is partially supported by NSF via grant CCF 1066471 508 Compliance SCORPION User Manual 29 7 Administrator Tools David In order to view Administrator Tools the user must have access to the administrator Gmail account Scorpion odu edu qmail com Viewing User Information 1 Click the Login link at the top right corner of the homepage 0 C3 SCORPION Fi OLD DOMINION a ag FP gt La OLA Pune Secondary Structure Prediction f mani Addres p mo a ad a e 2 Click on the big red button that reads Login With Google Log Into SCORPION Q Sign in with Google SCORPION User Manual 30 3 On the Google Account Chooser page login with the Administrator Gmail account Scorpion odu edu gmail com or an account that was created by the administrator Google x Choose an account gi anon WH y pama P aaj s PIu Da MA u Terr eod 10 Devid Eason jd Mid gert Mec lt lt A Pheer CoN 4 Once selected the browser will redirect to the homepage Now click the link at the top right corner User Data Welcome scorpion odu edu a gmail com 0 C3 SCORPION gt Po Ja OLD DOMINION Cortext based features 3 states Sccondary Structure Prediction IDEA FUSION News Horre Aaa Contac Instructions Que2. available Result J Title Date 5 05 14 Download the C3 Scorpion V 1 http www cs odu edu 411blue CS411 result php id 1 gt An Amino 2014 11 27 5 05 14 Latest training of the Scorpion gt sequence number 1 2014 12 01 Neural Network r x http www cs odu edu 411blue CS411 result php id 3 gt Sequence 2014 11 30 Showing 1 to 3 of 3 entries Previous 1 Next Developers Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu x This work is partially supported by NSF via grant CCF oon I 508 Compliance www cs odu edu 41 Iblue CS41 1 history php Filtering the history page Filtering can be done by entering in the sequence title into the search box Unmatched sequences will vanishing leaving the desired result This is shown below Welcome jackmuratore gmail com Profile History Logout O C3 SCORPION O LDD OMINION Context based features 3 states a Secondary Structure Prediction UNIVERSITY IDEA FUSION NO Home About Contact 8 23 14 New design new features still a man 6 Show 10 entries Search Sequence x the most accurate prediction service available Result S Title Date 5 05 14 Download the C3 Scorpion V 1 http www cs odu edu 411blue CS411 result php id 3 gt Sequence1 2014 11 30 5 05 14 Latest training of the Scorpion Showing 1 to 1 of 1 entries filtered from 3 total entries Previous 1 Next Neural Network Develope
3. Ea EE UNIVERSITY Secondary Structure Prediction IDEA FUSION N News Home About Contact Instructions 8 23 14 New design new Query Title Input your target sequence in fasta format a protein name tag is optional features still the most accurate l a a AS prediction service available Amino Acid database to retrieve results directly Sequence SAA EN A 5 05 14 Download the C3 Enter your email address Scorpion V 1 a Submit the form s When your results have been 5 05 14 Latest training of the predicted a webpage link to your Scorpion Neural Network UA 00 Oe AMARO SY Email Address jackmuratore gmail com Results will be sent here T Follow the link to display the results Clear Form Submit Sequence Required Developers Ashraf Yaseen Yaohang Li department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu 2 This work is partially supported by NSF via grant CCF soccer SO 508 Compliance Navigating the history page The history page shows a list of results A user can click on any of these results to navigate to the the result page for that specific sequence SCORPION User Manual 26 WW C3 SCORPION O LD D OMINION Context based features 3 states S Secondary Structure Prediction UNIVERSITY IDEA FUSION News Home About Contact 8 23 14 New design new features still wo Show 10 entries Search the most accurate prediction service
4. account 1 Click the Login link at the top right corner of the homepage C3 SCORPION Fe OLD DOMINION ii IP TE DRA MIDA Secondary Structure Prediction f mani Addres p mo Semi a e 2 Click on the big red button that reads Login With Google Log Into SCORPION S Sign in with Google SCORPION User Manual 3 On the Google Account Chooser page click Add account Google Choose an account Devid Eason e000 T fiends oct Bui Tem 14100 proa A om 2 David Eason A JONA m Midrugttt Mech Scorpion At odu y scorpion Ou SOGA 10m 4 Click Create an account Google 1 to add at nity uh SCORPION User Manual 6 Logging in as a standard user 1 Click the Login link at the top right corner of the homepage 0 C3 SCORPION EZ OLD DOMINION Context based features 3 states Ea a OLA PUSION Secondary Structure Prediction Emad Address r e Sini and e 2 Click on the big red button that reads Login With Google Log Into SCORPION Zi Sign in with Google SCORPION User Manual 3 On the Google Account Chooser page choose an account Non Administrative Gougle Choose an account 4 Once selected the browser will redirect to the homepage which will display a A welcome message with the user s email b The user s email in the sequence submission form c Navigation links to the user s profile and submission history Welcome deaso0074a odu edu Ww C3 SCORPIO
5. address The email address field is required a Fix Enter a valid email address into the email address field 5 Error Please enter a valid email address The provided email address must be a valid address a Fix Enter a valid email address into the email address field STING API Stanley 1 Deploying and hosting the STING API This can be used on any system runtime that supports PHP but accessible from all languages thatcan communicate over HTTP a Check Dependencies i PHP 5 4 li SQLite3 iii Composer Package Manager iv Apache 2 Check Tests a Run PHP Unit to see if test coverage still exists b Navigate to the root of the project c After the application is installed run the command vendor bin phpunit 3 Error Objects a Missing parameters All requests must have i mame the monicker that identifies the job to the submitter li title the genetic string of the sequence iii sequence the secondary protein string iv sanitization the status of requiring santization iv V email the email where the resulting prediction can be foudn SCORPION User Manual 36 b Sanitization i Requests that fall into these errors will be thrown and suggested for Sanitization 1 Special characters 2 White space 3 Upcase sequences li Replaces characters to make it fall under FASTA compliance for predictable sequences This area was intentionally left blank SCORPION User Manual 37 9 Sting A
6. intentionally left blank This area was intentionally left blank SCORPION User Manual 34 8 Troubleshooting This section details various issues and how to solve them Logins David 1 One issue that occurs is after logging in or logging out the user is presented with a blank screen To solve this a Goto Google com b In the top right corner click the current logged on profile c Click Log out d Close all browsers and try logging in again Analytics David 1 If the user is not presented with a graphical chart on the Analytics webpage or the page is blank a Click the Logout link at the top right corner of the webpage Goto Google com In the top right corner click the current logged on profile d Click Log out Close all browsers f Navigate back to the Scorpion Homepage g Click the Login link at the top right corner of the webpage h Log in with an administrator account 2 If the analytics page presents an orange button in place of the graphical chart a Click the orange button b Click Allow all c Ifthe chart still does not appear follow the steps in section 1 of the Analytics topic within this Troubleshooting library User Data Information David 1 If the user is not presented with a table of user information on the User Data webpage or the page is blank d Click the Logout link at the top right corner of the webpage e Goto Google com f In the top right corner click the current logged on pr
7. optional and will allow us accurate prediction service Amino Acid gt Sequence_ Al to search our database to EE ON Sequence ACDEFGHIKLMNPORSTVWYACDEFGHIKLMNPORSTVWYACDEFG retrieve results directly HIKLMNPORSTVWYACDEFGHIKLMNPORSTVWYACDEFGHIKLMN PORSTVWY Enter your email address features still the most 5 05 14 Download the C3 Scorpion V 1 Submit the form When your results have been ini s predicted a webpage link to 5 05 14 Latest training of Email Address ayaseen cs odu edu n eat a the Scorpion Neural Results will be sent you Network here Follow the link to display the results Clear Form Submit Sequence Required Developers Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu ST This work is partially supported by NSF via grant CCF 1066471 gt 508 Compliance This area was intentionally left blank SCORPION User Manual 16 4 Required Enter a valid email address 0 C3 SCORPION OLDDOMINION UNIVERSITY Context based features 3 states IDEA FUSION Secondary Structure Prediction Home About Contact Instructions 8 23 14 New design new Query Title Mas a Input your target sequence in fasta format a protein name features still the most tag is optional and will allow us accurate prediction service Amino Acid gt Sequence Al to search our database to avaliable Sequence ACDEFGHIKLMNPORS
8. title 0 C3 SCORPION OLDDOMINION UNIVERSITY Context based features 3 states IDEA FUSION Secondary Structure Prediction Home About Contact Instructions 8 23 14 New design new Query Title Demd i maaan features still the most ap tag is optional and will allow us accurate prediction service Amino Acid to search our database to available Sequence PUESTA BNS SD PREMIER retrieve results directly Enter your email address 5 05 14 Download the mi V4 Submit the form gt Corpion V When your results have been 5 05 14 Latest training of i A predicted a webpage link to 9 Email Address ayaseen cs odu edu your results will be emailed to the Scorpion Neural Results will be sent you Network i S Follow the link to display the results Clear Form Submit Sequence Required Developers Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu This work is partially supported by NSF via grant CCF 1066471 508 Compliance This area was intentionally left blank SCORPION User Manual 14 2 Optional Enter a sequence title Begin the sequence title with a greater than sign gt End the sequence title by hitting the Enter key on your keyboard 0 C3 SCORPION O L D DO MI N IO N Context based features 3 states IDEA FUSION Secondary Structure Prediction Home About Contact Instructions 8 23
9. title of the job for person archiving at a later time is a use case a curl X PUT http Localhost 9001 api v1 sting 18 d title ExpermintPaperlab H Content Type application json w n title ExpermintPaper Lab a DELETE Remove a job from the system calling the ID stored from the submission the client can remove jobs from the STING API See attached link for examples to interact with STING REST for a gt curl X DELETE http localhost 9001 api v1 sting 18 H Content Type application j son w An 0 ACCESS HTTP REST
10. www cs odu edu 41 iblue CS411 result php id 5 a Sent Mail Show details Drafts GmailTeX rich math F8 simple math F9 auto off 1248 1 deleted message in this conversation View message or delete forever rich simple heln amp about a Jack David Midnigh ae ait Tei 0 GB 0 of 15 GB used 2014 Google Terms amp Privacy Manage Last account activity 7 days ago Details SCORPION User Manual The result page shows both the Submitted amino sequence 1 and the secondary prediction sequence 2 C3 SCORPION Context based features 3 states Secondary Structure Prediction Home About Contact 24 Sign In Submission aaaaaaaaaaaaaadaaaaadaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa 1 Result RPXB 2 Developers Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu aS This work is partially supported by NSF via grant CCF oor SAA 508 Compliance This area was intentionally left blank SCORPION User Manual 25 5 History Jack Accessing the history page To access the history the user must first be logged in A logged in user will see the history link below Clicking it will navigate to the history page Welcome jackmuratore gmail com Profile History Logout C3 SCORPION IP O LD DOMINION Context based features 3 states
11. 14 New design new Query Title Tre Input your target sequence in fasta format a protein name A 3 tag is optional and will allow us accurate prediction service Amino Acid gt Sequence_Al to search our database to available Sequence retrieve results directly features still the most KR Enter your email address 5 05 14 Download the Submit the form C3 Scorpion V 1 When your results have been ini 5 predicted a webpage link to 9 05 24 Latest training of Email Address ayaseen cs odu edu your results will be emailed to the Scorpion Neural Results will be sent youl Network here Follow the link to display the results Clear Form Submit Sequence Required Developers Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu This work is partially supported by NSF via grant CCF 1066471 508 Compliance This area was intentionally left blank SCORPION User Manual 15 3 Required Enter or copy and paste an amino acid sequence The sequence should be at least 40 residues in length All alphabetical characters are valid residues excluding B J O U X Z 0 C3 SCORPION OLDDOMINION UNIVERSITY Context based features 3 states IDEA FUSION Secondary Structure Prediction Home About Contact Instructions 8 23 14 New design new Query Title ena Input your target sequence in fasta format a protein name i tag is
12. ETGGTN YLAPGGLSDSOLLLEPGDRSHWCVVAYWEEKTRVGRLYCVOEPSLDIFYDLPOGNGFCLGOLNSDNKSQLVOKVRSKIGCGIOLTR i EVDOGVWVYNRSSYPIFIKSATLDNPDSRTLLVHKVFPGFSIKAFDYEKAYSLORPNDHEFMQOPWTGFTVQISFVKGWGOCYTROF ISSCPCWLEVIFNSR name DogInfo title Canine email test cs odu edu time 2014 12 01 14 53 31 pred_status 1 sanitize yes pred_weights 58995976755878 665998 7858685798558999656966 786666965 7587756797759675598867785855858775978756999595586 9955 755 768988568889698 7559688 78567889698 75955598 785 76698 7897 798686866566896598698 79595 59668 766977795659559695 7985588585667 7678595685679758895695 79895685666559867 75555897697 886888976768898 7895999568556 765978696669 798968888897866 7566999 755895 789877579559996768 no z 79570658967759896997759877959666555896898865776597757786778965587775 pred_seq QIYV SEHLVCHHNEVIEKDNMNLMDKNPLMDQEWQTRNENLEKHEKKFIWRCSHSYSVGMDRYYRNFIESREICLPMRMWFNPYEQCSWI TASOWWTPDHOVMHS Y FHLVHKLRWYREKTDERAVMAFSVDYORRDONCHAWRYAMWGL FPWPHCWYRMPVECSCDIACWMQYAWT MFQWYKVRSEQFYLVCCAFVKWQTAEVHKMDWADTAKWOL TYLWNLTSOTHPWKWHAT T IMKNHFPVDWQAPQVMWQPAYRWGEDM TGIGFTFHDDMSEVFFLDNFEOYAFDHVHGTSITPITFLGGCLGTPFDDRCKKPWWHEKYWFTGCGVWPSIPCWORLWLPMAKCAD VMYHWFTFMTHHLPPRNAKKWLSRRALMFMYYYYLQCESCHLSPSCKTMKCETT IKDCWLMCRFYCRVSMTTPLCARA pred_ time 2014 12 01 14 53 31 ai This area was intentionally left blank SCORPION User Manual 40 PUT update updating a specific property of a job example updating the
13. IKLMNPORSTVWYACDEFGHIKLMN PORSTVWY Enter your email address a Submit the form a When your results have been predicted a webpage link to Email Address jjone191 odu edu your results will be emailed to Results will be sent you here a Follow the link to display the results Clear Form Submit Sequence Red bree cl Developers Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu This work is partially supported by NSF via grant CCF 1066471 508 Compliance This area was intentionally left blank SCORPION User Manual Amino acid sequence sanitation When entering your amino acid sequence into the protein sequence submission form you will have the option to utilize amino acid sequence sanitation Amino acid sequence sanitation enables automatic removal of whitespace invalid alphabetical characters and non alphabetical characters To utilize amino acid sequence sanitation complete the following submission form 1 steps using the amino acid input field of the protein sequence Enter or copy and paste a sequence containing whitespace and or invalid alphabetical characters and or non alphabetical characters 0 C3 SCORPION O LD DO MI N ION Context based features 3 states Wx PERRA Secondary Structure Prediction 8 23 14 New design new features still the most accurate prediction service available 5 05 14 Download the C3
14. N ig PP ae OLD DOMINION Context based features 3 states 7 gt DEA puni Secondary Structure Prediction s Query Tite Amino Acad Sequence Emad Address aip ead Mods oxy Menta ell te tert hare Cine Frem AE Sener SCORPION User Manual 8 Logging in as an Administrator 1 Click the Login link at the top right corner of the homepage 0 C3 SCORPION EZ OLD DOMINION Context based features 3 states Ea a OLA PUSION Secondary Structure Prediction Emad Address e Sini Aten e 2 Click on the big red button that reads Login With Google Log Into SCORPION Rt Sign in with Google SCORPION User Manual 9 3 Using the credentials provided log in using the default Administrator account Scorpion odu edu gmail com Google Choose an account LS 4 Eason OT gt 4 Once selected the browser will redirect to the homepage which will display a A welcome message with the user s email b The user s email in the sequence submission form c Navigation links to the user s profile and submission history d Administrative links for viewing user data and website analytics Welcome scorpion odu edu a gmail com C3 SCORPION Za N A OLD DOMINION eT ee P gt Sa OEA AD Secondary Structure Prediction News Hore Atos Cormac Instructions i 4 N m i Query Tife Amino Acid Sequence Emad Address gt scorpon Ody edudigmed com Heats al Se pert here nas Erem T
15. PGAPAGAQPAQPPSSYSLPLLLCKVFRWPDLRHSSEV KRLCCCESYGKINPELVCCNPHHLSRLCELESPPPPYSRYPMDFLKPTADCPDAVPSSAETGG TNYLAPGGLSDSQLLLEPGDRSHWCVVAYWEEKTRVGRLYCVQEPSLDIFYDLPQGNGFCLGQ LNSDNKSQLVQKVRSKIGCGIQLTREVDGVWVYNRSSYPIFIKSATLDNPDSRTLLVHKVFPG FSTKAFDYEKAYSLQRPNDHEFMQQPWT GFT VQISFVKGWGQCYTRQFISSCPCWLEVIFNSR name DogIinfo title Canine email test cs odu edu time 2014 12 02 00 26 44 pred_status 1 sanitize yes pred_weights 7655688999 796588 7598777 7559887659895586856668 7 8855597966998 76888 7898867985687 7556867695 7876867856775999586587 676656555857957867855967 76955 788895858867 769685 7678685868955566 7898677999585 78597975876756766956756958785696995985689859596555 5659867 7997559977568 7966685676887778765 76568986598 7858758587995 759568 787786568 769586555 786995896 765898 789855 756777978878985869 77785606867588976857655669958888866667 755666655655586785859698 This area was intentionally left blank 38 SCORPION User Manual 39 GET Get one using the unique job ID stored for the sequence GET Get all existing outstanding jobs in the STING API system curl http localhost 9001 api v1 sting 18 H Content Type application json w Nn id 18 seq MFRTKRSALVRRLWRSRAPGGEDEEEGAGGGGGGGELRGEGATDSRAHGAGGGGPGRAGCCLGKAVR GAKGHHHPHPPAAGAGAAGGAEADLKAL THSVLKKLKERQLELLLQAVESRGGTRTACLLLPGRLDCRLGPGAPAGAQPAQPPSSY 4 SLPLLLCKVFRWPDLRHSSEVKRLCCCESYGKINPELVCCNPHHLSRLCELESPPPPYSRYPMDFLKPTADCPDAVPSSA
16. PI Stanley This section details how to utilize the STING REST interface to interact with Scorpion Example can be issued over curl HOSTING The service can be hosted using any service that can run a PHP run time e lf over PHP 5 4 can run using language web server e Running on APACHE use the htaccess resource file Test using CURL POST insert curl X POST H Content Type application x ww form urlencoded d title Canine 4seg MFRTKRSALVRRLWRSRAPGGEDEEEGAGGGGGGGELRGEGATDSRAHGAGGGGPGRAGCCLGKAVRGAKGHHHPHPPAAG AGAAGGAEADLKALTHSVLKKLKEROLELLLOAVESRGGTRTACLLLPGRLDCRLGPGAPAGAOPAOPPSSYSLPLLLCKVFRWPD LRHSSEVKRLCCCESYGKINPELVCCNPHHLSRLCELESPPPPYSRYPMDFLKPTADCPDAVPSSAETGGTNYLAPGGLSDSQLLL EPGDRSHWCVVAYWEEKTRVGRLYCVQEPSLDIFYDLPQGNGFCLGQLNSDNKSQLVQKVRSKIGCGIQLTREVDGVWVYNRSSYP IFIKSATLDNPDSRTLLVHKVFPGFSIKAFDYEKAYSLORPNDHEFMOOPWTGFTVOISFVKGWGOCYTROFISSCPCWLEVIFNS R amp email test4 cs odu edu amp sanitize yes amp name DogiInfo http localhost 9001 api v1 sti ng id 18 W 7 fj SCORPION User Manual POST insert sanitization Sanitization flag is available to clean up special characters or invalid sequences caused from errors in translation of protein sequence yes curl http localhost 9001 api v1 sting 20 H Content Ty pe application json w An 4 1d 20 seq MFRTKRSALVRRLWRSRAPGGEDEEEGGGGGELRGEGATDSRAH GAGGGGPGRAGCCLGKAVRGAKGHHHPHPPAAGAGAAGGAEADLKAL THSVLKKLKERQLELL LQAVESRGGTRTACLLLPGRLDCRLG
17. Running Head Lab 4 SCORPION User Manual SCORPION USER MANUAL WV C3 SCORPION I OLD DOMINION Context based features 3 states Dd gt Secondary Structure Prediction IDEA FUSION Old Dominion University CS411 Blue Team Fall 2014 Authors David Eason Jasmine Jones Jack Muratore Stanley Zheng SCORPION User Manual 2 Table of Contents EUA CONN a VIG ie o o e iced en a o dd ed 3 AS A A Aan ahs unals Aina bic umlen aan eat aewaen A a oaelans 4 Os HOME Ja SmiNE incre eii net 11 A SUS A A o e E 23 Oe LS HO Yt GI DOUE COn ur e O S O A 25 0 USEF INOMaton Jana ilesini 27 Ti AQMINISTAator TOOS Dad aaa 29 o A A E 34 SS O A e A A A 37 SCORPION User Manual 3 1 Introduction David The Fall 2014 CS411 Blue team STING has worked with Dr Yaohang Li to design and build a new look with additional functionality for the SCORPION website at Old Dominion University This product includes a complete redesign of the website layout full 508 compliancy user login functionality with a self hosted database that integrates with Google logins and a RESTful API for programmatic access to the SCORPION neural network Detailed in the following sections are directions for using the website and RESTful API This area was intentionally left blank SCORPION User Manual 4 2 Logins David In order to log into the Scorpion Website a Google Gmail account is needed This can be created through the login process Creating a Gmail
18. Scorpion V 1 5 05 14 Latest training of the Scorpion Neural Network Input your target sequence in fasta format a protein name tag is optional and will allow us to search our database to retrieve results directly Query Title Title Amino Acid Sequence gt sequence number 1 aaaaaaaa aaaaaa aBaaaaaJaa aa0asaalaaaaXaaacaaZaaaaacaaaabacaaacaaajaaa oaaaauaaaaxaaaazaaaa a aaaaaGad aafataa 3331732453224 aaaaa aaaa Enter your email address Submit the form T73232320 gt 23M3231l1 gt 2l212f2laf2t2 gt When your results have been predicted a webpage link to your results will be emailed to you Email Address Results will be sent ayaseen cs odu edu here a Follow the link to display the results Required Clear Form Submit Sequence Developers Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu This work is partially supported by NSF via grant CCF oso ZA 508 Compliance This area was intentionally left blank SCORPION User Manual 20 2 Click the Submit Sequence Button An error message will appear informing you that the sequence contains whitespace and will ask if you would like it automatically removed 3 Click the button that says Yes to automatically removing whitespace OLD DOMINION INTERE TT Context based features 3 states DEAROSI N Secondary Structure Predi
19. TVWYACDEFGHIKLMNPORSTVWYACDEFG retrieve results directly HIKLMNPORSTVWYACDEFGHIKLMNPORSTVWYACDEFGHIKLMN PORSTVWY Enter your email address 5 05 14 Download the C3 Scorpion V af Submit the form a When your results have been ini predicted a webpage link to anal ae maining ot Email Address jjone191 odu edu your results will be emailed to the Scorpion Neural Results will be sent you Network ao l l here Follow the link to display the results Clear Form Submit Sequence Required Developers Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu This work is partially supported by NSF via grant CCF 1066471 508 Compliance This area was intentionally left blank SCORPION User Manual 17 5 Optional If you have made any errors and would like to start over you can clear all input fields of the form by clicking the Clear Form button 0 C3 SCORPION OLDDOMINION UNIVERSITY Context based features 3 states IDEA FUSION Secondary Structure Prediction Home About Contact Instructions 8 23 14 New design new Query Title me a Input your target sequence in fasta format a protein name features still the most tag is optional and will allow us accurate prediction service Amino Acid gt Sequence Al to search our database to avaliable Sequence ACDEFGHIKLMNPORSTVWYACDEFGHIKIMNPORSTVWYACDEFG retrieve results d
20. aft Satara SCORPION User Manual Logging Out 10 1 Once logged in click the Logout link at the top right corner of any webpage Welcome deaso007a odu edu C3 SCORPION ag OLD DOMINION Context based features 3 states ga NAO Secondary Structure Prediction i A 2 23 14 N Query Tife x Amino Aca Sequence 5 y v i e Emad Address deaX Pods ety Menta wil de vert Cese Frem abad Semene 2 The browser will be redirected to the homepage wy C3 SCORPION OLD DO i ION Context based features 3 states ra A naii Secondary Structure Prediction ES 1 23 14 New Query Tite a Amino Acad Sequence 14 f vial z Emad Address Benn aul te pert hee This area was intentionally left blank SCORPION User Manual 11 3 Home Jasmine Homepage features Upon visiting the home webpage the following features will be displayed a News column provides updates regarding Scorpion b Navigation bar 1 About link opens webpage with detailed information about Scorpion 2 Contact link opens webpage with contact information of Scorpion s creators Dr Ashraf Yaseen and Dr Yaohang Li c Protein sequence submission form provides the ability to submit a protein sequence d Instructions column provides instructions to use the protein sequence submission form e Sign in link provides the ability to sign into STING f 508 compliance link opens a PDF with AChecker validation of no known 508 c
21. ction PP gt News Home About Contact Instructions 8 23 14 New design new Query Title Title Input your target sequence in fasta format a protein name features still the most tag is optional and will allow us accurate prediction service Amino Acid gt sequence number 1 a to search our database to sunsa Sequence aaaaaaaa aaaaaa aaaaa aaaa i retrieve results directly aBaaaaaJaa aa0aaaalaaaakaaaaaaZacaaaaaaaabacaaacaaajaaa J a Enter your email address 5 05 14 Download the oaaaauaaaaxaaaazaaaa a aaaaalaf aafataa s 2 Submit the form C3 Scor ion V 1 Vaaslt7sR24GsanhaT7aRaaaGsaNari a alatalatassats gt Wi it h b x hen your results have been chiles inn The protein sequence contains whitespace sie e oik A atest training O F gt ER i Would you like whitespace automatically removed Yes your results will be emailed to the Scorpion Neural you Network i 5 avaseenG edt Email Address ayaseen cs odu edu Follow the link to display the Results will be sent results here Please enter an email address Clear Form Submit Sequence Required Whitespace will be automatically removed from your sequence A new error message will appear listing any invalid residues that are contained in your sequence The message will ask if you would like invalid residues automatically removed 4 Click the button that says Yes to automatically removing invalid residues E JA la SO OL D D O MI N IO N Context base
22. d features 3 states PEE E Secondary Structure Prediction News Home About Contact Instructions 8 23 14 New design new Query Title Title Input your target sequence in fasta format a protein name features still the most tag is optional and will allow us accurate prediction service Amino Acid gt sequence number 1 to search our database to Sequence aaaaaaaaaaaaaaaaaaaaaaaaBaaaaaJaaaaQaaaaUaaaaXx retrieve results directly available aaaaaaZaaaaaaaaaabaaaaaaaaajaaaoaaaauaaaaxaaaa Zaaaa a aaaaa ataaSataa e Enter your email address 5 05 14 Download the aaal2a34S5aaa6a7a8aaa9a0a a alalala a ata_a a C3 Scorpion V 1 atazata axa Submit the form a p E Invalid residues BJOUXZ When your results have been predicted a webpage link to your results will be emailed to 5 05 14 Latest training of Would you like invalid residues automatically removed the Scorpion Neural you Network E E E Email Address ayaseen cs odu edu Follow the link to display the Results will be sent results here Please enter an email address Clear Form Submit Sequence Required SCORPION User Manual 21 Invalid residues will be automatically removed from your sequence A new error message will appear informing you that your sequence contains non alphabetical characters and will ask you if you would like non alphabetical characters automatically removed 5 Click the button that says Yes to automatically re
23. ge In the homepage example your screen reader would be directed to the protein sequence submission form Skip to main content Sign In 0 C3 SCORPION IY OLD DO R IN ION Context based features 3 states IDEA FUSION Secondary Structure Prediction 8 23 14 New design new features still the most accurate prediction service available 5 05 14 Download the C3 Scorpion V 1 5 05 14 Latest training of the Scorpion Neural Network a Input your target sequence in Query Title Tie fasta format a protein name tag is optional and will allow us Amino Acid 1531a to search our database to Sequence AnS A RENA EBEMEEENS retrieve results directly Enter your email address Submit the form When your results have been E il Add z predicted a webpage link to mal ress ayaseen cs odu edu your results will be emailed to Results will be sent you here a Follow the link to display the results Clear Form Submit Sequence Required Developers Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu AAN T a UN This work is partially supported by NSF via grant CCF 1066471 4 lt 508 Compliance This area was intentionally left blank SCORPION User Manual 13 Submit a protein sequence To submit a protein sequence use the protein sequence submission form to complete the following steps 1 Optional Enter a query
24. ion of your estimated prediction time Please Click here to return to the protein sequence submission form Developers Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu This work is partially supported by NSF via grant CCF son E 508 Compliance This area was intentionally left blank SCORPION User Manual 23 4 Results Jack Obtaining a result from email After sequence is submitted a user will receive an email Below gmail is shown but any email service will work Google MEAN su HQ g Gmail y G More ero E i cial E Promotions WEJ COMPOSE La Primary Sam a0 re E So al ogle d Pla sj Inbox x D HTTP STING RESULT Click here for result http www cs odu edu 411blue CS41 1 result php id 5 Nov 30 Starred Important Sent Mail Drafts Gmail TeX rich math F8 simple math F9 auto off 1 2 4 8 rich simple heln amp about a Q Jack David Midnigh se 0 GB 0 of 15 GB used 52014 Google Terms 4 Privac Manage Last account activity 7 days ago Details Opening the email will display the message below and a link that will navigate to the result page Google EQ a HO S 1011 O a Y 3 3 Gmail a O compose STING RESULT W Miba Inbox HTTP lt http cs odu edu gt Nov 30 1 day ago A HTTP Starred to me Add to circles gi Important Click here for result http
25. irectly HIKLMNPORSTVWYACDEFGHIKLMNPORSTVWYACDEFGHIKLMN PORSTVWY Enter your email address 5 05 14 Download the l Submit the form C3 Scorpion V 1 a When your results have been 5 05 14 Latest training of r predicted a webpage link to f 3 Email Address jjone191 odu edu your results will be emailed to the Scorpion Neural Results will be sent you Network i s m Follow the link to display the results Clear Form Submit Sequence Required Developers Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu This work is partially supported by NSF via grant CCF 1066471 508 Compliance This area was intentionally left blank SCORPION User Manual 18 6 Click the Submit Sequence button to submit your form information to STING 0 OLD DOMINION UNIVERSITY IDEA FUSION C3 SCORPION Context based features 3 states Secondary Structure Prediction Home About Contact Instructions 8 23 14 New design new features still the most accurate prediction service available 5 05 14 Download the C3 Scorpion V 1 5 05 14 Latest training of the Scorpion Neural Network Query Title FE a Input your target sequence in fasta format a protein name tag is optional and will allow us Amino Acid gt Sequence Al to search our database to Sequence ACDEFGHIKLMNPORSTVWYACDEFGHIKLMNPORSTVWYACDEFG retrieve results directly HIKLMNPORSTVWYACDEFGH
26. moving non alphabetical characters U un We my ry cl N Context based features 3 states A Secondary Structure Prediction News Home About Contact 8 23 14 New design new Query Title Title features still the most accurate prediction service Amino Acid gt sequence number 1 e Sequence aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa available aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa a aaaa a a aaSataa s 5 05 14 Download the aaal2a34Saaa6a7a8aaa9a0a a aalala a ata_a a a aja a a lt a C3 Scorpion V 1 The protein sequence contains non alphabetical characters 5 05 14 Latest training of Would you like non alphabetical characters automatically removed the Scorpion Neural Network Email Address ayaseen cs odu edu Results will be sent here Please enter an email address Clear Form Submit Sequence Required Instructions Input your target sequence in fasta format a protein name tag is optional and will allow us to search our database to retrieve results directly Enter your email address Submit the form When your results have been predicted a webpage link to your results will be emailed to you Follow the link to display the results Non alphabetical characters will be automatically removed from your sequence The remaining sequence will be a valid sequence to submit to STING U Er El ye MINION Context based features 3 states RSIT Y EA FUSI N Secondary Structure Predictio
27. n News Home About Contact 8 23 14 New design new Query Title Title features still the most accurate prediction service Amino Acid gt sequence number 1 Sequence aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa available aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa 5 05 14 Download the C3 Scorpion V 1 5 05 14 Latest training of Email Address the Scorpion Neural ayaseen cs odu edu Results will be sent Network here Please enter an email address Clear Form Submit Sequence Required Developers This area was intentionally left blank D 7x Instructions Input your target Sequence in fasta format a protein name tag is optional and will allow us to search our database to retrieve results directly Enter your email address Submit the form When your results have been predicted a webpage link to your results will be emailed to you Follow the link to display the results SCORPION User Manual 22 Thank you webpage After you have submitted a protein sequence you will be directed to a thank you webpage which will display the following 1 An estimate of the duration time you should expect before you receive your prediction results 2 The email address to which results will be sent C3 SCORPION Context based features 3 states Secondary Structure Prediction Home About Contact Thank you Please check your email after the durat
28. ne SCORPION User Manual 32 6 Click on the big red button that reads Login With Google Log Into SCORPION Sign in with Google 7 On the Google Account Chooser page login with the Administrator Gmail account Scorpion odu edu gmail com or an account that was created by the administrator LO ale Choose an account Ens SCORPION User Manual 33 8 Once selected the browser will redirect to the homepage Now click the link at the top corner that reads Analytics Welcome scorpion odu edu a gmail com w C3 SCORPION i OLD DOMINION Ca a Context based features 3 states DEA MIO Secondary Structure Prediction meme fou Coras Instructions Query Tifo Amino Aces Sequence Emad Address sorpon ody edudigmeal com Heats at Se pert here a nas Erem Seiund Semen 9 The Browser will be redirected to the Analytics webpage Loading may take up to 10 seconds to get all of the page view data Welcome scorpion odu edu gmail com 0 C3 SCORPION Context based features 3 states O L D DO MI N 10 N ee aire Se IDEA FUSION AE Home About Contact 8 23 14 New design new features still the most accurate prediction service available m Page Views 5 05 14 Download the C3 Scorpion V 1 You are logged in as scorpion odu edu gmail com 5 05 14 Latest training of the Scorpion foot Neural Network Property Scorpion View All Web Site Data This area was
29. ofile g Click Log out h Close all browsers 1 Navigate back to the Scorpion Homepage j Click the Login link at the top right corner of the webpage k Log in with an administrator account Submitting a protein sequence Jasmine There are several errors message you can receive while submitting a protein sequence The following solutions can be used to fix each corresponding error 1 Error Please enter an amino acid sequence The amino acid sequence field is required a Fix Enter an amino acid sequence into the amino acid sequence field 2 Error Amino acid sequence must be at least 40 residues SCORPION User Manual 35 a Fix Enter an amino acid sequence into the amino acid sequence field that is at least 40 characters in length 3 Error Please make the amino acid sequence begin on a new line from the title There must be a newline character between your sequence title and your sequence lt may appear as though your sequence is on a newline because of word wrapping however the case may be that you only have a single space between your sequence title and sequence a Fix 1 Position your cursor at the end of your sequence title 2 Hitthe Enter key on your keyboard Amino Acid gt Seguence title Sequence ACDEFGHIKLMNPEKEKGHHFDFDRYSERASYTDFKFYDRHSDFHGF DEDFYTDRYREDCFREKLEFASDFREHKNHGFD Please make the amino acid sequence begin on a new line from the title 4 Error Please enter an email
30. ompliance errors U C3 SCORPION I O mr DO MI N 10 N Context based features 3 states IDEA ila Secondary Structure Prediction Instructions 8 23 14 New design new Query Title Title a Input your target sequence in fasta format a protein name features still the most tag is optional and will allow us accurate prediction service Amino Acid gt 153la to search our database to available Sequence aa ena rn E A CS retrieve results directly Enter your email address 5 05 14 Download the C3 Scorpion V 1 Submit the form When your results have been 5 05 14 Latest training of Emai Address C predicted a webpage link to the Scorpion Neural ayaseen cs odu edu your results will be emailed to Results will be sent you Network here Follow the link to display the results Clear Form Submit Sequence Required Developers Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu Ar This work is partially supported by NSF via grant CCF ooa ZA 508 Compliance f SCORPION User Manual Skip to main content If you are using a screen reader and would like to skip to the main content of the page complete the following steps 1 Hit the Tab key on your keyboard until the Skip to main content link appears 2 Hitthe Enter key on your keyboard Your screen reader will be directed to the main content of the pa
31. rs Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu w This work is partially supported by NSF via grant CCF 106647 OF 508 Compliance This area was intentionally left blank SCORPION User Manual 27 6 User Information JACK Accessing the user profile page A logged in user has access to the profile page The link will be shown in the top right hand corner Clicking on the link will navigate to the profile page Welcome jackmuratore gmail com Profile History Logout 0 C3 SCORPION O LDD OMINION Context based features 3 states aa UNIVERSITY Secondary Structure Prediction IDEA FUSION News Home About Contact Instructions 8 23 14 New design new Query Title a Input your target sequence in fasta y format a protein name tag is optional features still the most accurate and will allow us to search our prediction service available Amino Acid database to retrieve results directly Sequence q Enter your email address 5 05 14 Download the C3 Submit the form Scorpion V 1 When your results have been 5 05 14 Latest training of the predicted a webpage link to your Scorpion Neural Network results will be emailed to you Email Address jackmuratore gmail com a vt id Follow the link to display the results Results will be sent here Clear Form Submit Sequence Required Developers Ashraf Yaseen Yaohang Li Departmen
32. ry Tifo n Amino Aces Sequence 4 i Y Emad Address soorpon dy edudigmead com Menta al Se pert here liar Erem Taft Cad This area was intentionally left blank SCORPION User Manual 31 5 The browser will redirect to the User Data webpage A table displays all user data available including Email Address Number of Submissions Name Location Phone Number Type of user Administrator or Standard The table may be sorted on preference by clicking the corresponding column header and specific items may be searched for by entering text into the search box eee ea Welcome scorpion odu edu a gmail com 0 C3 SCORPION a gt O LD DO MINION Context based features 3 states wes Secondary Structure Prediction IDEA FUSION Show HO e MO e rt of Emad Submisel Name Location Phone Admin c54 tObivoteamibgmat com 0 fue Admin Hortok_ VA Yes denso0007 odu edu 0 No p y Georga Up in the r s 4 J Joorgapetsonddgmad com 0 Jalana USA 1214 No kmuratored i com 1 pito Uunchburg Y 732 589 1638 No jackmu agma Masratore ynchourg Va 32 5 JO escorpion odu edufbgmal com 0 Yos Google analytics 1 Click the Login link at the top right corner of the homepage Y C3 SCORPION OLD DOMINION cc ore cage sted FP E Context based features 3 states IFE DEA PUSON Secondary Structure Prediction Query Tife Amino Acs Sequence Emad Address Derby all te pert rare Cina Frem AUTE Sere
33. t of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu xt a has This work is partially supported by NSF via grant CCF 106647 D 508 Compliance The profile page will list optional information that the user can fill out Filling out this information will help improve SCORPION The email 1 label is not changeable and will display the current logged in email Name 2 Location 3 Organization 4 and Phone 5 can be changed or be left blank Profile information previously entered will be displayed as it is below concerning the user s Name 2 Welcome jackmuratore gmail com Profile History Logout 0 C3 SCORPION O LD D O MINI O N Context based features 3 states L E ms Secondary Structure Prediction JNIVERSIT AY m IDEA FUSION ay 8 23 14 New design new features stil the most accurate prediction service Email jackmuratore gmail com available 5 05 14 Download the C3 Scorpion V 1 Name saci coin 5 05 14 Latest training of the Scorpion Location Neural Network Organization Phone Save Cancel Developers Ashraf Yaseen Yaohang Li Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu x w This work is partially supported by NSF via grant CCF oor 508 Compliance SCORPION User Manual 28 Changing profile information To change information the user just enters the new information on the field Below is an e
34. xample of changing the Location After ther user changes the field pressing Save will store the information and show a confirmation dialog Welcome jackmuratore gmail com Profile History Logout 0 C3 SCORPION O LD D OMINION Context based features 3 states s Secondary Structure Prediction UNIVERSITY i IDEA FUSION EN Home About Contact 8 23 14 New design new features still the most accurate prediction service a i siti i n Email jackmuratore gmail com vai a Name Jack Muratore 5 05 14 Latest training of the Scorpion Location Lynchburg VA Neural Network P Organization Phone Cancel w Department of Computer Science Old Dominion University Contact yaohang at cs dot edu dot edu This work is partially supported by NSF via grant CCF 1066471 D 508 Compliance Below is the confirmation dialog after saving Clicking okay will finish the history change x P ai iiaii shen eee gt si CORPION O LD D OMINION Context based features 3 states pa Secondary Structure Prediction UNIVERSIT Y 7 IDEA FUSION News Home About Contact 8 23 14 New design new features still Developers Ashraf Yaseen Yaohang Li the most accurate prediction service Email jackmuratore gmail com available 5 05 14 Download the C3 Scorpion V 1 Name PACE PARES 5 05 14 Latest training of the Scorpion Location Lynchburg VA Neural Network Organization Phone Save
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