Data Sets
Informatics
- The City of Hope's Center for Informatics supports diverse and computationally intensive needs in data retrieval, curation, integration, annotation, automation, dissemination, visualization, and training. The city of hope center for informatics utilizes several platforms in the collection of data including but not limited to POSEIDON, Honest Broker Form, Registry of Hope and Natural language Processing.
High Performance Research Computing
- The High Performance Research Computing Center (HPRCC) is responsible for supporting the computational biology, genomics, informatics, mathematical oncology, metabolomics, proteomics and system biology programs. This group provides customized research support for high performance computing clusters, and research servers.
- If you have any questions that are not answered or need additional help, please submit a ticket to the ITS Service Desk and include in the first line "Sys - Admin HPRCC"
- There are currently clusters that are available for City of Hope researchers, including Apollo High Computing Clusters.
Protocol Database
- Protocols.io, which can be used by researchers/labs to manage and share protocols. Library licenses a variety of protocol publications, print and video. *Site license paid by City of Hope. For installation of software on your City of Hope computer, contact the IT department.
Internal Data Sets
- To request internal patient data to be pulled, complete the Honest Broker Form and follow the instructions on the form for submitting the request.
- There are 12 different registries - Lymphoma, Leukemia, Multiple Myeloma, Sarcoma, Urology, GYN, Breast, TMI, Infectious Disease, Upper GI, Colorectal, etc. To request information from the existing Disease Registries, complete the Honest Broker Form
- Cytobank can be used for the analysis of multiplex flow cytometry data. It can be used for data repositories for all flow cytometry data and raw images (microscopy, gels etc). See iLab to learn how to order high dimensional flow cytometry machines, and other equipment.
Online Survey Tools
- REDCap is a secure web application for building and managing online surveys and databases. While REDCap can be used to collect virtually any type of data in any environment (including compliance with 21 CFR Part 11, FISMA, HIPAA, and GDPR), it is specifically geared to support online and offline data capture for research studies and operations.
External Data Sets
- Epic Cosmos is a repository of data of over 135 million patient records from across the Epic community, giving access to healthcare data that is representative of the U.S. population.
- NCI GDC
- NCBI Datasets
- EMBL-EBI datasets
- NCI DTP
Information Storage and Folders
- To create a network folder on the COH server, submit an IT Service Request ticket with the following information included: 1) the file path where you want the folder created; and 2) decision to allow "read/write/modify" access covering all subfolders.
- To store large amounts of data, submit an IT Service Request ticket. Typically, network folders can store up to 50 TB of data, but IT experts prefer storage size to be around 20 TB or less for optimization.
- Transferring files can be performed via the standard drag and drop functionality when working with other COH colleagues. For external collaborations, submit an IT Service Request ticket. There are various options available and exceptions may need to be granted, such as SecureFTP (sFTP), FileZilla (client application), and Dropbox.
*If you are currently logged into your COH account and having issues accessing the Research Portal, select "Submit General Service Request" to submit a Service Request ticket or call our IT Service Desk at (626) 218-4357 or 8-HELP (84357).
