WIXLIB

Biostatistics Computing Seminar SeriesComputing Resources @ PennSarah J. Ratcliffe, stat-research/SJRatcliffeAssociate Professor of BiostatisticsDepartment of Biostatistics and EpidemiologyCenter for Clinical Epidemiology and BiostatisticsSeptember 2013

O VERVIEWPenn ResourcesFile ManagementData AnalysisWeb SitesMobile DevicesCCEB ResourcesWeb SitesFile ManagementData AnalysisSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 20132 / 35

P ENN R ESOURCES File ManagementB Penn BoxB SharePoint *NEW*B Secure ShareB Encryption *NEW* Data AnalysisB REDCapB SoftwareB Amazon Web ServicesB PennHPC Web Sites Mobile DevicesSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 20133 / 35

P ENN B OX Information: http://www.upenn.edu/computing/box/ Direct login: https://upenn.box.com/login Similar to Dropbox Cloud service forB Sharing files and folders within & outside PennB 50GB limitB Sending large files (max. 5GB per file) as download links; not emailattachments Access information from a variety of popular operating systems,browsers, and handheld devicesB ”My Account”ñ ”Get Box Sync”B ”Use my company’s single sign-on creditals” for syncing withPennKeySarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 20134 / 35

P ENN B OX ( CONTD .) Data Types OK to store:B Non-Confidential University DataB FERPA DataB Human subject research data - Only with IRB approval Data Types NOT OK to store:B HIPAA DataB Social Security NumberB Credit Card DataB ITAR/EAR Penn working with Box to become HIPAA compliantB Must ensure auto-sync is not activated on protected dataSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 20135 / 35

S HARE P OINT Will be available 3rd quarter, 2013 html#sharepoint http://office.microsoft.com/en-us/sharepoint/ Web-based Microsoft product for collaboration, documentmanagement, web building, etc. Types of files that can by store to be determined.Sarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 20136 / 35

S ECURE S HARE re/ Encrypted web-based application for sharing files within Penn.B Can securely transfer FERPA or HIPAA regulated dataB Safe alternative to email, FTP, portable devices Maximum file size: 100MB File available for 30 days, or end of day once downloadedSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 20137 / 35

E NCRYPTION S OFTWARE http://www.med.upenn.edu/pmacs/encryption.shtml Required on all portable computing / media devices withsensitive or confidential data PGP Whole Disk Encryption (WDE)B Protects data if computer lost or stolenB Does not protect if user is logged in. PGP Netshare EncryptionB Encrpytion for data stored on windows networked file shares. Travel restrictions and export controls apply to PGP encryptiontechnology.Sarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 20138 / 35

P ENN R ESOURCES File ManagementB Penn BoxB SharePointB Secure ShareB Encryption Data AnalysisB REDCapB SoftwareB Amazon Web ServicesB PennHPC *NEW* Web Sites Mobile DevicesSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 20139 / 35

R ESEARCH E LECTRONIC D ATA C APTURE (REDC AP ) https://redcap.med.upenn.edu/ Free, secure, web-based data management Build surveys and databases Export data to Excel, PDF, SAS, Stata, R, SPSS Reporting capabilities REDCap TrainingB on trainingB In Person: Sign-up to receive notice of training. Recording of pasttraining sourcePage.shtmlSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201310 / 35

S OFTWARE Discounted or free software available from:B ect/about.htmlB Computer omputerstore/B Office of Software Licensing s/softwarelicenses/ Student pricing obtained with a valid student ID.Sarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201311 / 35

S OFTWARE : P ENN C ONNECT Free DVD of recommended and supported software Also available online with valid PennKeyB http://www.upenn.edu/computing/product/ Released each fall and spring Current software includes:B Virus protection - SymantecB Email setup - Kerberos, ThunderbirdB Terminal Emulation / SSH - HostExplorer, SecureCRTSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201312 / 35

S OFTWARE : C OMPUTER C ONNECTION re/ Discounted software purchased with personal funds for home use Microsoft Product Examples:B Office 365 University - 4 years for 1 user license 79.99B Windows 7 Professional - 299.99 Abode Product Examples:B Acrobat Professional - 55.00 (MSRP 449.00)B Creative Suite 6 - 199.00 (MSRP 1,299.00)B Photoshop - 169.00 (MSRP 999.00) Student Statistical Software (with valid ID)B SAS - 65.00 per yearB Matlab - 99.00Sarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201313 / 35

S OFTWARE : S TATISTICAL S OFTWARE Discounted software for home use via OSL See Clay Wells for help with ordering Matlab single user license:B New - 300B Annual renewal - 200 SAS:B Annual license - 85B Student annual license - 65 (Computer Connection)Sarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201314 / 35

S OFTWARE : S TATISTICAL S OFTWARE ( CONTD .) Stata:B GradPlan pricing for students, faculty staff at Penn; teachingfaculty at CHOP or HUP.B Discounted academic pricing for non-teaching faculty / staff atCHOP or HUP.B GradPlan purchased online -pickup/Stata/IC - 189 (perpetual); 98 (annual); 69 (6-month student)Stata/SE - 395 (perpetual); 235 (annual)Small Stata - 49 (annual); 32 (6-month); students onlyStata/MP (2-core) - 695 (perpetual)Sarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201315 / 35

A MAZON W EB S ERVICES (AWS) http://www.upenn.edu/computing/isc/aws/ Dynamically scalable computing, storage Should NOT be used for sensitive data Fee-for-Use serviceB Cost based on per hour (or part there of) usageB Free to upload files; cost to store or downloadB Price calculator available athttp://calculator.s3.amazonaws.com/calc5.html Free instance available to test / try Licensing of needed software is a user costB Cannot currently use software licensed to department See Clay Wells for help with account, setting up an instance, etc.Sarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201316 / 35

H IGH P ERFORMANCE C OMPUTING (P ENN HPC) html#pennhpc Available 2nd quarter, 2013 Fee-for-Use service Can be used for protected dataSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201317 / 35

P ENN R ESOURCES File ManagementB Penn BoxB SharePointB Secure ShareB Encryption Data AnalysisB REDCapB SoftwareB Amazon Web ServicesB PennHPC Web Sites Mobile DevicesSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201318 / 35

SOM W EB S ITES http://www.med.upenn.edu/pmacswebteam/ Free web hosting, design, maintenance Available to departments, centers, institutes, grad groups, labs, ororganizationsB Not available for personal, individual or commercial sites 30 MB quota Must conform to SOM design standardsSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201319 / 35

P ENN R ESOURCES File ManagementB Penn BoxB SharePointB Secure ShareB Encryption Data AnalysisB REDCapB SoftwareB Amazon Web ServicesB PennHPC Web Sites Mobile Devices *NEW*Sarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201320 / 35

M OBILE D EVICES ategory/mobile-0 Should not store confidental or protected files/data Can be configured to access email via -activesync-eas Can be configured for WiFi access via esources/category/pennnet-and-airpennnetSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201321 / 35

O VERVIEWPenn ResourcesFile ManagementData AnalysisWeb SitesMobile DevicesCCEB ResourcesWeb SitesFile ManagementData AnalysisSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201322 / 35

CCEB R ESOURCES Web SitesB Help WikiB Biostatistics Research @ UPenn File ManagementB File ServersB Public Data Data AnalysisB Linux ServersB GridB SoftwareSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201323 / 35

I NFORMATION W EB S ITES Help Wiki Biostatistics Research @ UPenn Maintained by Clay WellsB Ph: 215-573-4231B Location: 635 BlockleyB Email: clayw@upenn.eduB Can help with obtaining any Penn / CCEB resourceSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201324 / 35

H ELP W IKI https://dbe.med.upenn.edu/secure/wiki/ Help using CCEB resources. Eg.B Configuring home email, AirPennNet wireless, remote desktop,secureCRTB Changing passwords - intranet, unixB Policies and formsB Oracle helpB Getting started on Linux, the GridSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201325 / 35

B IOSTATISTICS R ESEARCH @ UP ENN https://dbe.med.upenn.edu/biostat-research/ Create web sites:B -series-biostat-research-siteB Personal biostatistics research sitesB Project related sitesB Upload public files - size / type limits Resource pages available after PennKey loginB Computing seminars - schedule, handoutsB Software - helpful links for statistical softwareB Educational - guidelines, LaTeX dissertation template, timetable, etcB PhD Directory - get a protected, backed-up location to store yourresearch de/249Sarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201326 / 35

CCEB R ESOURCES Web SitesB Help WikiB Biostatistics Research @ UPenn File ManagementB File ServersB Public Data Data AnalysisB Linux ServersB GridB SoftwareSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201327 / 35

F ILE S ERVERS Network windows and linux mounted file storage Files backed up daily, weekly, monthly Project directoriesB Manage all files associated with a single projectB Control access and user privilegesB Created using ormdistributed.pdfSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201328 / 35

P UBLIC D ATA Drive a\ Shared, read only, repository of public datasets Readme file for directions on how to add dataSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201329 / 35

CCEB R ESOURCES Web SitesB Help WikiB Biostatistics Research @ UPenn File ManagementB File ServersB Public Data Data AnalysisB Linux ServersB GridB SoftwareSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201330 / 35

L INUX S ERVERS Current servers:B s280r1 - remote loginB biolinux - R, GaussB bioapps - R, Stata/MP, Matlab, GaussB app441 - SAS, S-Plus Can handle large datasets Commands can be batched to run at given times More information ?title Unix/Linux Help TopicsSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201331 / 35

G RID For running large, time consuming jobs Commands should be tested on linux servers first Batch jobs can be submitted via bioapps, biolinux, app441 Statistical software: R, SAS, Stata, Matlab More information ?title Grid HandbookSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201332 / 35

S OFTWARE tle CCEB Software Complete listing of software available within CCEB (costs mayapply)B Valid desktop, laptop, home and student usage under licensingB Number licenses for key served (shared) softwareB License expiration dates Links for installing commonly used free softwareSarah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201333 / 35

U SEFUL L INKS Penn Computinghttp://www.upenn.edu/computing/ Penn Medicine Academic Computing Service (PMACS)http://www.med.upenn.edu/pmacs/ CCEB Help Wikihttps://dbe.med.upenn.edu/secure/wiki/ Biostatistics Research @ rah J. Ratcliffe (sratclif@upenn.edu)Computing Resources @ PennSeptember 201334 / 35