2015-04-10 User Manual Progeny
Contents
1. Trtted sies This tone cordains Web sias that you trust not to damage your computer or dete a ae eee E S O gt Click on the button Sites A window will open where you can add any sites that you wish to be in the trusted zone Be sure to remove the check by the entry Require server verification https 2015 04 10 User Manual Progenypdf 13 W PROGENY 4 E N acre Make it yours XMIRE s ra You can add and remove Wieb sites from this tone All Web stes in thes zone vel use the rone s security setings Add this Web site to the zone Web stes gt Enter the site of interest in the line provided http euromotor umcutrecht nl Site URLs can be typed in directly or entered by copying and pasting Note that it is not an https site and that the appropriate box is unchecked After entering the site click the Add button Trusted sites You can add and remove Web sites from this rome All Web sites in Ges none wi use the rone s security settings Add thes Web site to the zone hipija artes com Ca Web stes _ Require server verification hipa for al sites in the zone cane The site is now added to the list of trusted sites You can open the site by typing https euromotor umcutrecht nl in Internet Explorer note the additional s 2015 04 10 User Manual Progenypdf 14 O PROGENY QA A Project MINE pPria euTSMOTOR Progeny Databa2. E Global ID Al I S syste Individual Name E Date of birth 01 General DOB gender Sex gender at birth 01 General DOB gender 3 Sort Optignal Type Field Direction 1 Globi Ascending 2 E Ingvidual Name Descending f Query Optional Type Field Operator Value AND OR Date of birth i 01 01 1980 02 02 1950 03 0 y v gt Query It is possible to search for or select data export for only selected multiple individuals in the database One can search on for example Global ID numbers or date of birth or on any data field The different ID numbers or dates of birth mm dd yy need to be separated by comma s And the operator should be selected One can play with the operator key and make all sorts of selections gt Once the spreadsheet output has been selected the spreadsheet format can be saved as a standard so it can be used again at a later stage J Run Load Frit Main x H New Ind Spreadsheet x Fields Search for Fields amp Data Folders c yole 2015 04 10 User Manual Progenypdf 10 W PROGENY Make it yours M in E SOPHIA gt Click Run to create the spreadsheet and obtain all the data gt After obtaining the results you can still edit the again by clicking Edit if Edit Load Fmt Save Fmt Main x New Ind Spreadsheet x gt You can also count the number of results by clicking Count gt You can export the results b
3. O PROGENY Make it yours aM in E Bru A User Manual Progeny ALS database Prior to gaining access to the Progeny ALS database the principal investigator of the participating ALS research center organization is required to sign a data sharing agreement to ensure confidentiality of the data and prevent use of data without prior consent of the owner of the data Each contributing center remains owner of its own data including clinical data biological samples and analyses of biological samples This user manual will help first time users of the Progeny ALS database in the context of the EuroMOTOR project the SOPHIA project Project MinE and any other future collaborative ALS research projects The manual shows how to open up the part of the database assigned to your center organization and depending on your security level how to create new individuals input data and extract specific data for analysis There are two types of database users Researcher and Assistant Assistants have read and write access to the database and are the people who input all patient control data Researchers have read only access to the database and can extract anonymous data only Every Monday morning from 9 00 until 12 00 hrs the Progeny ALS database will be down for maintenance and updates Please do not try to enter the database during this time thank you Logging in gt Open your internet browser and go to euromotor umcutrecht
4. the new individual does not already exist in the database by for example searching for the Individual ID first in the top right of the screen before creating the new individual You will now also see that the newly created individual has been added to the folder 1 Clinical Data with an automatically assigned individual Global ID number 1626 amp Ug Hew Ind Man x Individuals a E web euromotor_db Global ID Folder Mame Individual Mame B 9 Ireland O 1626 1 Clinical Data IR Test123 1 Clinical Data IR C 2 EuroMoToOR IR C 3 SOPHIA IR This individual has also been automatically added to the other two folders 2 EuroMOTOR and 3 SOPHIA in the database amp ip Hew Ind Ind Main x Individuals 8 web euromotor_db Global ID Folder Mame Individual Name 9 Ireland HH 1626 2EuroMOTOR IR Testis C 1 Clinical Data IR gt 2 EuroMOTOR IR CI 3 SOPHIA IR 2015 04 10 User Manual Progeny 3 ra AC WZ PROGENY XM project D i INE s p SD it yours FILA ot gt You can also double click on the new individual in any of the three folders and start filling in specific data for this individual The data will be saved automatically The data folders Personal and core clinical data can be added in folder 1 Clinical Data The data sheet in this folder contains several tabs Personal Data Clinical Data Genetic Testing ALS FRS R ECAS Cognitive ECAS Behaviour Under
5. 0 Exaeniner intennber Weel L bere A We L Eume A viet 4 Pammer R inbenmater Welt 5 Eimine A Wait 6 Examiner AJ Mak 6 Erama AJ ivirarater Jet uwm evbereater viat 7 Ename A fet 6 bamine When filling in tables you always start with adding a row to the table see button Add Row in lower lefthand corner or right click on the table and select Add Row The folder 4 Extra is currently empty but has been added in case extra questions from your center organization need to be added to the database in the future Data extraction mainly for Researchers Progeny allows extraction of specific data from individuals into a spreadsheet gt Click on the arrow to the right of Ind Spreadsheet in the top left hand corner of the screen E New Individual Main x Individuals 2015 04 10 User Manual Progeny 5 W PROGENY QA A Project AMINE s eraa CUIOMOTOR gt Select Build Spreadsheet or if a spreadsheet format has been created already select Spreadsheet formats gt Select and drag the data fields you want to extract the data from to the Type Field area in Columns on the right hand side of the screen Data fields in Progeny The data fields to select from are organized in 5 main folders System fields 01 General 02 Clinical 03 Projects and 04 Institutes 2015 04 10 User Manual Progenypdf 6 WZ PROGENY QA A Project A
6. Datasheet Basic Information Biometrics Ancestry Residential History Smoking History Alcohol Consumption Hormones Medical History 1 Medical History 2 Trauma Injury Other Hospitalisatio Sport Drug Use Prescription Drug Us Parents Brothers an Uncles al Basic Information Register Enter Date of Survey 15 02 13 Basic Information Smoking History Biometrics Alcohol Consumption Ancestry Hormones Residential History Medical History 1 amp 2 2015 04 10 User Manual Progeny 4 q project Mink S PHIA WZ PROGENY Trauma Injury Disorders Parents and Grandparents Other Hospitalization Disorders Father s side Sport Drug Use Disorders Mother s side Prescription Drug Use Physical Activity Parents Brothers and Sisters Occupations Uncles and Aunts When double clicking an individual in the 3 SOPHIA folder the data sheet for this project appears It has several tabs one for each of the different subprojects within SOPHIA e g Munix neuropathology It also has a tab called Personal Data which is a copy of the data filled in earlier in the 1 Clinical Data folder and only repeated here as a double check A Q Man i giesa individual Datasheet Pernod Guta bet MUM peurnccamoiagy MUNIX data C iari tabet Waa Vat Dwie Examrmnmedaie SLS FRG R api MUNIC ER BUR AD MUR E MUN T MUN MUR ED CRP EP CUAP AD C YER 0 Euainer Al Vee 0 Eumo J inbrarater Vet
7. MINE s eraa Run Load Fmt Save Fmt Main x H New Ind Spreadsheet x Fields Search for Fields Q Columns amp Data Folders Type Field system Fields O individual Data Folders Si 01 General G 02 Clinical E 03 Projects i 04 Institutes 9 Ireland I Test institute CE Import Fields P Pedigree Data Folders There are some standard fields in the Progeny database which you can choose They are in the folder System Fields Global ID An unique number automatically given by Progeny to each new individual Individual Name A unique number or name linking Progeny to your own system or database In the folder 01 General the data fields for contact details date of birth and gender and different project numbers EuroMOTOR SOPHIA etc can be found In the folder 02 Clinical the data fields for all core clinical data can be found personal data clinical data genetic testing ALS FRS R and ECAS In 03 Projects the data fields specific to projects can be found such as the data fields for EuroMOTOR CRF data fields and SOPHIA MUNIX data fields neuropathology data fields etc In the folder 04 Institutes subfolders have been created for each center organization only visible to that centre organization in which data fields specific to that centre organization are assembled Sometimes data has been collected in a table format like for example the El Escorial data 2015 04 10 User Manual Progenypdf 7 q proj
8. Personal Data an Assistant is able to fill in and see non anonymous data under the heading Contact Details this data is hidden from those logging in as Researchers kal fad ri gt a _ fel e ie Logged in as Assistant m e Logged in as Researcher E ATAN w jis indiridual Datan Perra Data Pesona Persona Data l Personal Data Phi wih for Hesir F E iae of seth T Shabe of Ceti EJ Date of bett J A Sra Hara AL Mok Pirra mr A Fha hiara E rajag ert or A Pore arre cet I Pree are Al ete A reed Projects Projects Individual 5 pan wit in Dur D a nividual k par vtr a ID numbers 1D numbers fishes Ti Pebtusl rare Joba D dsa rame F CeT pif Tent Progery AJ Tirotiro Ti A tucrenbe EursMiorcR BuroMO TOR Ay UL irae 1 A WD read Extra ID F Extra iD IR The assistant can indicate in relation to which project data for this individual is assembled by ticking the box for the appropriate projects currently EUroMOTOR SOPHIA Project MinE and or PYRAMID Extra ID s can be filled in here as well For each individual entered into the Progeny ALS database the data fields in the folder 1 Clinical Data should be filled in as completely as possible as a minimum When double clicking an individual in the 2 EuroWMOTOR folder the data sheet for this project appears It has several tabs following the standard CRF as defined in EuroMOTOR A a Undo Redo Main x SyTestiz3 x Individual
9. ect PROGENY Mine SPHA Main x iy Testi uw Individual Datasheet F Recently U i j Perdnaldva Clinteal dala Genetic lesinga ALS FRS H CAS OGHA ECAS beh Clinical data E Date of diagnosis Respiratory function tests FVC is prefered E Table FWE E Diagnosis E Other diagnosis namely Date FV FVC Lires FVC of predicted Testing not feasible E Co morbidity 1 A Co morbidity 1 other E Co morbigiiias A Co morbidity 2 other SL AddRow Copy Row SL Delete Row Table El Escorial Daie El Escorial El Escoria category Number of affected family members with ALS MND and FTD O eid Row Copy Row 1 Delete Row p First degree Parents brothers sisters sons and daughters EALS MND first degree E FTO Dementia first degree Site of onset E Date of onset Fie agnostic delay days Other family members E ALS MND other E FTO Dementia other E Site of Onset A Notes Family histo The data fields to select for data extraction can be recognised as follows when building the spreadsheet 2015 04 10 User Manual Progenypdf 8 MinE Make it yours E s px lA O PROGENY Mi B Run Load Fmt Save Fmt Main x New Ind Spreadsheet x Fields Search for Fields 9 Columns Data Folders Co morbidity 2 other a Type led Path Date of Death Date of diagnosis Date of ECAS at diagnosis Date of endpoint gt 23h NIV day Date of onset 02 Clinical Diagnosis system Fie
10. eld level security Class based security can be defined even at the field level Roles and permissions can be setup to determine what rights a given category of users has to modify or view data fields e Folder level security The ability to read add delete and modify is controlled at the folder level Security applies to folders throughout the software including data field folders This flexibility is ideal for SOPHIA where one group of users is not able to read or to modify another group s data Folder level security makes it possible for several institutions or groups to share a single database e Database level security The user can set the level of security on the database by restricting functions such as the ability to add delete or modify an individual folder as well as the ability to add delete or modify a data folder e Password expiration Passwords have a forced expiration every 180 days after which they must be changed The new password is validated to not contain the old password e Password naming conventions Enforced passwords are required to be 6 characters long contain both letters and numbers and cannot include the User ID e External access protection Access to the Progeny database from outside the Progeny application is restricted to the Progeny administrator User ID e Login auditing Each login to the database is audited The User ID operating system application host name login date and logout date are recorded for
11. em Fields f Sex gender at birth individual Data Folders 01 General 3 contact details DOB gender 3 Projectnumbers 9 02 Clinical 3 03 Projects ma nA Inctitiutac ia Contact For any functional or technical questions regarding the use of the Progeny ALS database please contact Hermieneke Vergunst or Bas Middelkoop by sending an email to h vergunst umcutrecht n or b m middelkoop umcutrecht nl 2015 04 10 User Manual Progenypdf 12 MinE Make it yours E s puia Q PROGENY Min Appendix A To open the login page of the database please follow the next steps to add the page to your trusted sites and try opening the page once more by typing https euromotor umcutrecht nl in the Internet Explorer note the additional s gt Open Internet Explorer and go to Tools Internet Options Security F Internet Options a Home page A ou can change which page to use for pour home page Address about blank Temporary interest fied F Pages you view on the hiemel are stored in a specia folder Fy hor quick wiewang later History A The Hitory folder contains inks to pages you ve vished for Fe quick access to recently viewed pages Dartokeenpogesnhitey 20 5 a __Forts _ Uerguoges recensar ox Ca gt Click the Security tab and choose the Trusted Sites icon Internet Options Select a Web content zone to apecty is securly settings
12. every successful and unsuccessful login Progeny Web Application Security Features The Progeny Web Application depends on and builds on top of the security features available in the desktop application To protect the application against web specific security vulnerabilities a security layer was added with the following protections e Server generated user tokens have expiry time e SQL injection attack protections e Treat all requests from internet as untrusted e SSL encryption of all request progeny web application e Cross site scripting protection 2015 04 10 User Manual Progenypdf 15 MinE WD PROGENY Make it nE gan e Strong public cryptographic algorithms e Measures against session stealing The Progeny ALS database is set up behind a firewall This ensures that any attack on the web server does not necessary result in a direct compromising of the database since there will be another security layer for the attacker to get past 2015 04 10 User Manual Progenypdf 16
13. gn Out Creating a new individual and adding data Assistants only If you are an Assistant and want to start filling in data for an individual patient or control you first have to create a new individual in the database in the folder 1 Clinical Data gt Make sure the folder 1 Clinical Data is highlighted and click on New Ind in the top left hand corner of the screen amp ig Hew Ind Qmanx Individuals 8 El 9 Web euromotor_db Global ID Folder Mame Individual Ma S 0 Ireland 1 Clinical Data IR CI 2 EuroMOTOR IR C 3 SOPHIA IR gt A new screen will pop up Fill in the individual name This needs to be an unique and anonymous or coded name or number for the individual it can also be the number of your 2015 04 10 User Manual Progeny 2 O PROGENY q project ade SMINE sgena Bog E OTOR own database for example Than indicate whether the individual is male or female tick the box that says Open on save and click save If needed we can always set up a second ID field to record any additional database system number Add New Individual Gender Male C Female Unknown ga Web euromotor _db E Ireland 1 Clinical Data IR E 2 EuroMOTOR IR Q 350PHIA IR gt The template for the newly created individual in this example the individual called Test123 will open up and data can be added The data will be saved automatically gt Do make sure that
14. lds amp individual Data Folders 1 Table El Escorial Date El Escorial 02 Clinical 01 Core clinical data 2 Table El Escorial El Escorial category 02 Clinical 01 Core clinical data 01 General gt 01 clinical data Diagnostic delay days Tbl subfields ECAS result at diagnosis First symptom Cognitive or behavioural First symptom Weight loss FTD Dementia first degree FTD Dementia other If tracheostomy date of endpoint tracheos Not deceased no tracheostomy and no gt Notes Family History Al Sort Optional A Other diagnosis Type Field Bs Side onset e EJ Table El Escorial Date El Escorial Table El Escorial El Escorial category fo Query Optional EJ Table FVC FVC Litres E Table FVC Testing not feasible Table SNIP Date SNIP Table SNIP SNIP cmH20 Table SNIP SNIP cmH20 Table SNIP Testing not feasible Type Field The subfolder called Tbl subfields can be ignored these subfolders should never be used to extract data from tables gt Once the data fields have been selected the order of which can still be adjusted by clicking the green arrows on the right hand side of the box one can also sort or query the data output by adding the data fields to sort or query on to the boxes below and select the sorting order or query type 2015 04 10 User Manual Progenypdf 9 O PROGENY OR A Project OME spra Columns Add to sort or Add to query Type Field
15. nl without www If you encounter problems with opening the login page e g an invalid response message please follow the steps described in Appendix A to add this page to your trusted sites This should resolve the problem WZ PROGENY Progeny 8 205 8914 01 Username Connection euromotor_db Change Password Login gt Log in using your username and password which you can obtain by contacting the Progeny admin The homepage of the database will open which looks like this 2015 04 10 User Manual Progeny 1 O PROGENY Make it yours XMIRE s pun CUIOMOTOR amp C B https euromotor umeutrecht nl amp Ug Hew Ind Ind WO Main x Individuals 8 S E Web euramotor_db Global ID Individual Mame Ireland CI 1 Clinical Data IR C 2 EuroMOTOR IR 9 3 SOPHIA IR This example shows what an Irish user would find The folder reland and the subfolders 1 Clinical Data IR 2 EuroWOTOR IR and 3 SOPHIA IR These folders and the data that is put in are only accessible to the people in your center organization and to the persons with general database administration rights Hermieneke Vergunst and Barbara Thuss ALS Centre The Netherlands In the upper right hand corner of the screen it is possible to view and edit your user profile and to sign out of the system ie Thuss Barbara Thuss Barbara bj thuss umcutrecht_nl View Profile Si
16. se Security Statement The Progeny system has clinical data security at its core and meets the robust compliance required by the US HIPAA standards for managing sensitive clinical data http www hhs gov ocr privacy The WEB system separates the application server that is exposed to the outside world and the database server that remains behind the UMCU firewall All data transferred between the database WEB application and the outside world is encrypted and secured using SSL connections https Progeny Security Features e User identification and authentication The User ID and encrypted password control who has database access e Auditing With two forms of auditing available the Chain of Custody audit maintains a record of transactions performed on the database while the Field audit records the values that are updated displaying old and new values for every modification Both audits time stamp each event with a date time and User ID In addition the database engine has extensive auditing available in the form of log file operations e Discretionary access control features The actions that a user can carry out while connected to a database are defined within the User ID e User and user class definitions Users are assigned to class definitions to determine the roles and permissions throughout the software General permissions such as access to spreadsheets the data warehouse markers and form design are also assigned to the User ID e Fi
17. y clicking Export In the pop up box specify the delimiter and make sure that you tick the boxes Include Column Headings and Export One Row per Individual The latter is to make sure that results from data tables are exported in one row instead of in multiple rows Settings Text Tab Delimited Text Comma Delimited Text Other Excel inline Options Include Column Headings Export Table Rows Only Export One Row Per Individual Set up of the main screen On the start page of the database you can select to view a few useful standard identifiers of your own choice 2015 04 10 User Manual Progenypdf 11 q project Vx Procenv SMInE spna Bow 9l MOTOR amp Ug Hew Ind Ind Orn Individuals Enter Search 8 E re Web euromotor_db Global ID Folder Name Individual Name Date of birth Gender Gi Ireland T 1626 1 Clinical Data IR Test1z3 M Plisi Jump To Row Add To Sort P 1 Clinical Data IR 2 EuroMOTOR IR ss Add Column 3 SOPHIA IR Insert Column Delete Column gt The individuals can be sorted or filtered using these identifiers by right clicking on one identifier and choosing an option gt One can easily add or delete identifier columns by right clicking on a column clicking Add insert column and selecting which data field to show from the list of input options a Field Chooser I Data Folders Date of birth syst
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