Lab 4- User Manual Green Team 12/2/13 Version 1
Contents
1. Lab 4 User Manual Green Team 12 2 13 Version 1 Table of Contents MTOdUCt ON SN CO Ud NR odd Od Odd Rd ddd dodd 3 SAUD S CO 0 PF FT EEE AB ARO A P NR Y FY TON 3 Unregistered US a O dL NA a A CG OG 8 How to Resister Usenass si Dd bd aa a 10 User Ea SS O OR I R WR NN HD NT AR ene FR 12 ACM ATOT EOS SF YN Dosah o FU HYNN DE 19 Table of Figures Pour e Starup oeiee ineen Uw od GU do y da A DG tob te o odst z Rs 4 Figure 2 Startup Page Register and EOgIn aed aoa Yd 5 EiG1re 5 Startup Page T IDS i GY Y E EVA p n 5 Figure 4 Startup Information Tab cc ccc cece cece area DD DD YY Yad 6 Fisure o Startup Reference TAB a dd Db BU sd 68 DA 6 Pisure 6 Startup Statistics Tab ic cccsicsccaravecsonscorsaiscdpearerasstspeawersasotagnnes 7 Freie Startup Help Gap s snad moa ore Fd a hnala mama ane 7 Fi ure o Startup Contact BAB ae a A added ko ky Baden asn 8 Figure 9 Startup Sequence Text FOrms 0 cece cece LL cece Y Y eee YY uad 8 Figure 10 Unregistered User Submit Button 0 cece FY YY Y nn aaa 9 Figure LL Email and Solution En Kc aaa ON NON SOUND DOD Un SOAR 10 Figure 12 Register User Country Drop Down Box 11 Figure 13 Register User Submit and Clear Buttons YY YYYYY Ya ll Fisune IA 0 er Woot SC Tasa a AD E Y A ER Yd 12 Figure 15 User Email and Password Text Felds Y YY YF Ya 13 Figure 16 Login page Submit and lear2. on Total seguences submitted 0 If at any time you need to get back to the submit page just click on the link in the top left of your browser When you are finished click log out in the top right corner Figure 22 User Home Page Reference Contact Link To logout of your account the Log Out link 1s at the top right of the page Submit Page References Contact su cf de veda Welcome mrajs001 odu edu This is the user account page This is where you can check the progress of your currently pending or completed seguences Joined Dinosolve on Total seguences submitted 0 If at any time you need to get back to the submit page just click on the link in the top left of your browser When you are finished click log out in the top right corner Figure 23 User Logout Button When you click Log Out you will be automatically logged out and redirected to the logout page 18 Submit Page References Contact Register A ENO R DEAE S JN PA 5 u f de SAU MAN AN AI You have successfully logged out Please close your browser Figure 24 Logout Screen Administrator Utilities Page David Crook Main Page The main page of the Administrator s page has 3 tabs as shown in Figures 26 29 and 32 The first tab is a tab labeled Users This button redirects you to the Users page which will allow you to ban search for or change the password for a user The second tab 1s a tab labeled website stats
3. or Contact information click on the respective tabs located in the red box DMINION pap Cs CID Cf Ci CdD Ce UNIVERSITY pone W O D OLD DOMINI ON COMPUTER SCIENCI CDV Ce premio INFORMATION REFERENCES STATISTICS HELP CONTACT Title DinoSolve Sequence E mail Figure 3 Startup Page Tabs wr OLD BON Other Projects Login CSaCDAGa ade OLD DOMINION COMPUTER SCIENCE DinoSolve Figure 4 Startup Information Tab n OLD DON cd Cb lt 1 r Cd pp DVD S In this work we introduce an approach of enhancing disulfide bonding prediction accuracy We firstly derive the first order and second order mean field potentials according to the amino acid environment around cysteine residues from large number of cysteine samples The mean field potentials are integrated as context hased scores to estimate the favorability of a cysteine residue in disulfide bonding state as well as a cysteine pair in disulfide bond connectivity These context based scores are then incorporated as features together with other sequence and evolutionary information to train neural networks for disulfide bonding state prediction and connectivity prediction Our computational results have shown that the context based scores are effective features to enhance the prediction accuracies of both disulfide bonding state prediction and connectivity prediction The 10 fold cross validated accuracy is 9
4. the tag at the beginning However the tag with the protein chain name will be used to search our database where results can be retrieved directly The method will take your input and later a link to the results page will be sent to your e mail Follow the link there to display the results mail Ifthe inputsequence does not contain any CYS residues or only one CYS residue then the results will be displayed instantly on the same page result If more than one CYS is found in your input then the method will process your query A sample output is shown below Figure 7 Startup Help Tab NW TYMINION pc a Cs gt u gt cI gt X lt fOCi gt d gt ce UNIVERSITY FA On rose a A OLD DOM LALL ON INFORMATION REFERENCES STATISTICS HELP CONTACT Ashraf Yaseen Department of Computer Science DinoSolve Old Dominion University Norfolk V ayaseen cs odu edu Dr Yaohang Li Department of Computer Science Old Dominion University Norfolk V yaohang Pcs odu edu ARMS Department of Computer Science Old Dominion University Norfolk VA ARMS website Le as adis a alu dde df an hn ab an la an Figure 8 Startup Contact Tab register Login m CAD CD GG De D OLD DOMINIC JN COMPUTER SCILENCI OLD DMINION N if INFORMATION REFERENCES STATISTICS HELP CONTACT gt Di noSolve Sequence required Figure 9 Startup Sequence Text Forms Unregistered Use
5. 0 8 at residue level and 85 6 at protein level in classifying an individual cysteine residue as bonded or free which is around 2 accuracy improvement The average accuracy for disulfide bonding connectivity prediction is also improved which yields overall sensitivity of 73 42 and specificity of 91 61 My Account Log Out CSO CUD CID CF Ci CdD CeD 4 DinoSolve Figure 5 Startup Reference Tab INFORMATION REFERENCES STATISTICS HELP CONTACT Dinosolve Implementation is described in this paper Ashraf Yaseen and Yaohang Ll Enhancing Protein Disulfide Bonding Prediction Accuracy with Context based Features accepted at BIOT12 Biotechnology and Bioinformatics Symposium My Account Log Out n NION cfc gt kbce lt UNIVERSITY a Cb A OLD DOM d NION COMPUTE TENGE d gt W INFORMATION REFERENCES STATISTICS HELP CONTACT DinoSolve Figure 6 Startup Statistics Tab ww ION amp amp c uo ll cf gt Ci gt d gt ce UNIVERSITY em b gt CD OLD DOMINION DDD INFORMATION REFERENCES STATISTICS HELP CONTACT How to use Dinosolve a The method consists of two stages DinoSolve 1 Cysteine bonding state prediction 2 Connectivity prediction m logo On the main page input your target sequence in fasta format and provide your e mail address Those two input fields are mandatory fasta Note you can also submit your query without
6. 4 0 0293 sybil melton31313 gmail com ee CCPYSILVGRVFTTWPTRYWRTDFSYOECTAEHTLPDHFACFDCPWYI Pagei23 gt E Figure 19 User Login Select Seguence and Resubmit Button To view your seguences that have not been completed click the Pending tab 16 Submit Page References Contact su CD DG De D EZ 00 Welcome mrajs001 odu edu This is the user account page This is where you can check the progress of your currently pending or completed seguences Joined Dinosolve on Total sequences submitted 0 If at any time you need to get back to the submit page just click on the link in the top left of your browser When you are finished click log out in the top right corner U Figure 20 User Login Pending Tab The pending seguence page will show you the title seguence and submission time Submit Page References Contact OYODOOO b D o Submission Title Seguence Time 2013 12 CNTIHTMLNLKEGNERTSDNKKWEPLGHYNKGLLNAMDKKLGLFTDVYIFSFRPCKNVVTYSCTESIHKYVKCV 06 09 40 41 Figure 21 Pending Seguences At any time 1f you wish to return to the Submit Page view References or contact Dinosolve administrators links are available on the top left hand of the page 17 Submit Page References Contact syw db MO bed o Welcome mrajs001 odu edu This is the user account page This is where you can check the progress of your currently pending or completed seguences Joined Dinosolve
7. Administrator Select User Reset Password or Ban Submit Page References Contact oo eo bed Je m Figure 30 Website Stats Tab All users Search Users Search Users 24 United States Alexandria1 1 United States Virginia Beach 1 United States Norfolk173 20 Total pageviews 175 total visits 31 Country City Pageviews Visits Figure 31 Website Statistics submit Page References Contact ss pe bed m eo All users Search Users Search Users Figure 32 Administrator Sequences Tab 25
8. FREE EL RR DD ann 13 Fiore 7 PasswWOrd RST aY akad ze dano a Y TARO OO B aaa dk vu 14 Figure 18 User Login Page Complete Tab asota svadasodaca ed GORN 15 Figure 19 User Login Select Sequence and Resubmit Button 16 Eisure 20 User Lorin Pendine Taps oii ser ee DR GYD NA O Y OR 17 Proure I Pendina egHeiic OS si WY AA GYNYG eau UG 17 Figure 22 User Home Page Reference Contact Link FFY YN 18 Eizure 2 User Lopout Button aea oe aU OU ubude A OAOD COG 18 Pisure 24 LOL ut SCEE osada DO obe zato este 19 Piue 25 Admis trator Baec ca yd neue OND GUDD 22 Figure 26 Administrator Users Button ssssssusessessrseserserseserseseesessesee 22 Figure 27 Administrator User SeatcCh lt lt 444454444000 0000000600000 A AAA A AAA 23 Figure 28 Administrator Search All USETS 0000000 23 Figure 29 Administrator Select User Reset Password or Ban en 24 Figure 30 Website Stats TaD i YY ae l 24 Proure gt l Web Tad st Ic Gu cts ound une GU O yn NAG BOD IREE TOEO 25 Figure 32 Administrator Sequences Tab YY FYRFYFYR e FR YRR e cece ee eeeeenes 25 Introduction Michael Rajs Allocated Resource Management Services ARMS configures a distributed resource management system Sun Grid Engine to handle resources on a cluster The cluster being used 1s going to be modified on a research website application called Dinosolve Dinosolve is a disulfide b
9. Learn more Sent Mail Drafts 20 gt Pe Disulfide Bonding Prediction Circles e Dear User Thanks for using the Disulfide Bonding Prediction Server Your job has been finished on the server Priority Please follow the link below to display your predction results More v Click here to display prediction results o MS Best Regards Disulfide Bonding Prediction Team m David Crook o afaga004 Dodu edu o jking058 o Jordan Heinrichs o Justin Maynard 2 Samantha Puckett 0 32 GB 1 of 30 GB used 2013 Google Terms of Service Privacy Policy Program Policies Manage 2 Last account activity 1 hour ago manage Powered by C oogle Details Figure 11 Email and Solution Link How to Register as a User Scott Pardue The register user screen located in figure 15 will provide a drop down box for you to provide your location Right below that there is a series of text boxes named email password and confirm password that you will need to fill out to become a registered user for Dinosolve Figure 15 Once you fill out everything click the Submit button located below the text boxes to be processed into the database as a user If you just want to clear the form you can click the Clear button located to the right of the Submit button Figure 16 10 gt SubmitPage References Contact tegister Login Password required Confirm Password Location required Already have an
10. This tab will redirect you to a page he can use to view the total hits or hits by country for Dinosolve The third tab is the Sequences tab The sequences tab will redirect you to a page where you can view pending Jobs in the gueue or completed jobs currently stored in the database Users Page The users page links to two pages that provide different functionality Shown 1n figure 25 The first option on the left will redirect you to the all users version of the users page where 1t simply lists every user 10 at a time The second option will let you search for a specific 19 user using their email address On either version you will be provided with a table of users Each user on the table will have a checkbox next to them along with their number of seguences personally submitted and whether or not that user is an admin At the bottom of the table are numbers that redirect the user to more pages of users Below the pages are the Ban Set admin and Reset Password buttons The ban button will ban all of the users with a checked checkbox next to them The set admin button lets you set all users currently checked to administrator status or vice versa The reset password button will let you reset the password of the selected users shown in Figure 29 The users page 1s on the search users version by default Search Users Page The search users page is the search version of the users page It is made for
11. account Login A Figure 12 Register User Country Drop Down Box SubmitPage References Contact register Login S Adghnirtan E mail Password required Confirm Password Location required gt oo Already have an account Login Figure 13 Register User Submit and Clear Buttons 11 User Login Sybil Melton Submit Page References Contact E mail Password Submit Forget your Password Figure 14 User Login Screen To log into Dinosolve follow these steps 1 Enter your email into the text box Register Login 12 m 2 Enter your password into the password text box submit Page References Contact Register Login D d OOWO gt gt Submit Forget your Password Figure 15 User Email and Password Text Fields 3 Click the Submit button To clear your inputs from the login page click the Clear button submit Page References Contact Register Login E mail Password Forget your Password Figure 16 Login page Submit and Clear 13 m If you forget your password click the Forgot your Password Link It will bring you to the following page Submit Page References Contact NADD P am s u MEAN DOG lt p d KE ITN CT 8 d Enter your email and a new password will be sent to you Email Figure 17 Password Reset To reset your password follow these steps 1 Ente
12. e all of the checked seguences from the gueue Completed jobs administrator page The completed jobs administrator page will show you all of the jobs that were completed and stored Each of the jobs will be shown in a table where the email address of the user who submitted 1t title seguence results submission time and a checkbox are shown 1n different columns Below the table is a resubmit button that will resubmit all checked sequences back into the queue for parsing 21 m Submit Page References Contact OL AO All users Search Users Search Users EA Figure 25 Administrator Page Submit Page References Contact m DOOD EST RR All users Search Users Search Users Figure 26 Administrator Users Button 22 Ju DOB Website onsi Sequences All users Search Users gt Search Users Figure 27 Administrator User Search submit Page References Contact bed Website anal Sequences Search Users Search Users Figure 28 Administrator Search All Users 23 Submit Page References Contact All users Search Users Sequences Submitted Administrator a smelton cs odu edu a rau 9 NH see 2 w C spbimetonatars qnaicom 9 jordan heinrichs88 gmail com F mrajs001 odu edu spardue cs odu edu spardue rs odueas o majs00 oduedu i Figure 29
13. ences submitted 0 If at any time you need to get back to the submit page just click on the link in the top left of your browser When you are finished click log out in the top right corner 15 Figure 18 User Login Page Complete Tab The Completed page shows you the title seguence connectivity state bonding state and submission time of the seguence Completed seguences can be resubmitted 1f there 1s an algorithm update To resubmit seguences follow these steps 1 Click the check box next to the seguence 2 Click the Resubmit button An email will be sent to you with the results when the job is completed pod eepeeop Users a Seuuences completed jobs Submitted by Title Sequence 0 2338 s j Jess CSWITSCMFHWLSLAWHYMWPCOHMEKAHKSIFMSWMTIKTTPFM Oh ee sees smelt008 odu edu CSWITSCMFHWLSLAWHYMWPCOHMEKAHKSIFMSWMTIK M 0 2085 08 42 22 C1 lt gt C73 0 8683 2013 11 23 smelt008 odu edu sybil CNTIHTMLNLKEGNERTSDNKKWEPLGHYNKOLLNAMDKKLOLFTDVYJFSFRPOKNVVTYSCTESIHKYVKOV gt 7991 pa F a s new C5 lt gt C29 0 9466 2013 11 24 JIsybil melton31313 amp gmail com EYVWCINGWNESGHPPHKODRCEVVELECNTCISSYRSLPIALTS exec c29 03 50 23 0 9780 c32 0 9811 c2 0 5388 C lsybil melton31313 amp gmail com s MCTLTSHGGTOPRANYYSTINGCEKLTVVONFETPWPCKKEFWHFVNNYEFOFMTY Cym p kol z execc C38 0 8294 0 6290 03 53 17 C38 0 8565 C1 0 1131 c2 0 0326 C29 2012 11 24 0 3782 04 08 42 C41 0 2990 C4
14. formation for the user to click on and view For instance the Information tab will provide general information about Dinosolve provided in Figure 4 The Reference tab provides information of how Dinosolve was implemented Figure 5 The Statistics tab describes and shows the accurate statistics of Dinosolve Figure 6 The Help tab is a set be step explanation of how to use Dinosolve Figure 7 And the Contact tab lets the user email and view the major contributors that helped to create Dinosolve Figure 8 Below the five buttons are specific text fields named Title Seguence and Email and which are the reguired fields that must be filled out in order for a disulfide bond seguence to be processed then solved and emailed to the user Figure 9 m aa O IDMINION UNIVERSITY Other Projects DinoSolve Register Login Ci Cd Ce OLD DOM IN LON COMP Bay ae NCI INFORMATION REFERENCES STATISTICS HELP CONTACT Title TH E mail Clear Figure 1 Startup Page To register or login to the site simply click the Register or Login word located in red TOMINION SODODODOGDLDOS UNIVERSITY P m Cb d gt OLD DOM 4 NI ON COMPUTER ELENG ODwWoOm INFORMATION REFERENCES STATISTICS HELP CONTACT Title DinoSolve Sequence E mail Figure 2 Startup Page Register and Login To access Information References Statistics Help
15. ond predictor that 1s important to scientists and researchers all over world because it helps them speed up their research to create new cures for diseases new bioenergy and new drug designs for pharmaceutical companies In this user guide you will find helpful steps on how to register as a user how to submit a seguence how to login as a user or administrator and how to navigate easily through the Dinosolve website The user guide will also help you in using and viewing special features associated with being a user or an administrator Startup Screen Jordan Heinrichs The start up screen is the first thing you see when you open up the website Figure 1 It can be loaded from any number of browsers such as Firefox Google Crome or even Internet Explorer The page has a user friendly scrolling ability and the display is designed to fit any computer monitor The start up page contains a register button and a log 1n button that are located at the top right of the page Figure 2 When the register button is clicked a person will be redirected to a separate page and allowed to register to be a Dinosolve User When the log 1n button 1s clicked a person will be redirected to a separate page allowed to log in as a Dinosolve user The start up page contains five buttons named Information References Statistics Help and Contact which are located in the center of the page right below the logo Figure 3 These buttons provide general and helpful in
16. r Adam Willis Submitting a sequence 1 Input a title for your sequence in the box labeled Title This is optional 2 Input a seguence in the box labeled Seguence Seguence must be 40 characters long and contain two cysteine residues 3 Input your email address in the box labeled E mail This is how you will receive a link to the prediction results 4 Click submit comp Register Login IOMINION jn s u Cl gt fOCi gt cd gt ce gt UNIVERSITY p EN Other Projects b 1 d OLD D OM alk N L ON COMPUTER SCIENC O OO O INFORMATION REFERENCES STATISTICS HELP CONTACT S gt KC DinoSolve acy a D m Cb D OLD DOM n NI ON COMPUTER SCLENC INFORMATION REFERENCES STATISTICS HELP CONTACT Title DinoSolve Sequence E mail Figure 10 Unregistered User Submit Button Viewing Prediction Results 1 You will receive an email with a link confirming your prediction results are ready 2 Click the link to view your results OLD DOMINION Eca Michael mas a Share Click here to enable desktop notifications for Old Dominion University Mail Learn more Hide Mail a o a m gt More 1 of 4 258 gt O Disulfide Bonding Prediction Results Inbox x A Related Google Page Inbox 2 364 dinosolve cs odu edu 12 13 AM 0 minutes ago 4 Old Dominion n Starred a mei OLDDOMINION Follow Important A This message was not sent to Spam based on your organization s request
17. r your email that you used to register with Dinosolve 2 Click the Submit button A randomly generated password will be emailed to the email address you registered with If you click submit without entering an email you will see the following error message Email cannot be blank If you click submit and enter the wrong email you will see the following error message Email not found If you click submit and you have used Dinosolve but have not registered you will see the following error message 14 Not a registered user Once successfully logged in you will be directed to the user account page This page provides you links to view your pending and completed submitted seguences and change your password To change your password click the Change Password link You will re directed to the change password page lt Need screen shot gt Enter your new password and click the Submit button If your password 1s successfully changed you will be redirected back to your account page If the new password entered does not conform to the password reguirements you will see the following error message Password must be between 8 and 16 characters To view your completed seguences click the Completed tab Submit Page References Contact Welcome mrajs001 odu edu This is the user account page This is where you can check the progress of your currently pending or completed seguences Joined Dinosolve on Total segu
18. when you need to find a specific user The search 1s performed by entering an email address using the field after search users and clicking the submit button shown 1n Figure 27 After searching for a user if there is a person with the email address being searched the table will update with the user and his specifics in it If there is not a person with the email address being searched currently registered the user will not show up All Users Page The all users page will show all users 10 at a time divided by clickable page numbers Website Stats page This page will show you the current hits of the Dinosolve website in total and by city shown in Figure 30 Above the table are total pageviews and total unigue visits The table itself 20 will show each country in the first column and its individual pageviews and unique visits in the second column Administrator Seguences Page The administrator seguences page is where you can interact with jobs currently pending or stored on the server There are two different versions of this page This page starts on the Pending Jobs in the gueue page by default Pending Jobs administrator page This page will show you the jobs currently in the gueue The jobs are shown in a table where their title seguence connectivity state bonding state submission time and a checkbox are shown in different columns Below the table is a delete button that when pressed will delet
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