Analytics users https://informatics-analytics.dfci.harvard.edu/ en PathML tools for computational pathology https://informatics-analytics.dfci.harvard.edu/pathml-tools-computational-pathology <span class="field field--name-title field--type-string field--label-hidden">PathML tools for computational pathology</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/2" hreflang="en">DF/HCC</a></div> <div class="field__item"><a href="/taxonomy/term/1" hreflang="en">DFCI</a></div> <div class="field__item"><a href="/taxonomy/term/3" hreflang="en">Outside participating sites</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/155" typeof="schema:Person" property="schema:name" datatype="">biodata</span></span> <span class="field field--name-created field--type-created field--label-hidden">Sat, 06/01/2024 - 19:32</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p><strong>PathML objective is to lower the barrier to entry to digital pathology.</strong></p> <p>Examples:</p> <ol dir="auto"> <li><a href="https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/loading_images_vignette.ipynb">Load over 160+ different types of pathology images using PathML</a></li> <li><a href="https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/stain_normalization.ipynb">H&amp;E Stain Deconvolution and Color Normalization</a></li> <li><a href="https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/workflow_HE_vignette.ipynb">Brightfield imaging pipeline: load an image, preprocess it on a local cluster, and get it read for machine learning analyses in PyTorch</a></li> <li><a href="https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/multiplex_if.ipynb">Multiparametric Imaging: Quickstart &amp; single-cell quantification</a></li> <li><a href="https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/codex.ipynb">Multiparametric Imaging: CODEX &amp; nuclei quantization</a></li> <li><a href="https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/train_hovernet.ipynb">Train HoVer-Net model to perform nucleus detection and classification, using data from PanNuke dataset</a></li> <li><a href="https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/pathml_gallery.ipynb">Gallery of PathML preprocessing and transformations</a></li> </ol> <p>More information at: <a href="https://github.com/Dana-Farber-AIOS/pathml" rel=" noopener" target="_blank">https://github.com/Dana-Farber-AIOS/pathml</a></p> <p>in a hurry? &nbsp;&nbsp;<em>docker pull pathml/pathml &amp;&amp; docker run -it -p 8888:8888 pathml/pathml</em></p> </div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/30" hreflang="en">Analytics users</a></div> <div class="field__item"><a href="/taxonomy/term/20" hreflang="en">Basic researchers</a></div> <div class="field__item"><a href="/taxonomy/term/11" hreflang="en">Clinical researchers</a></div> </div> <div class="field field--name-field-access-and-support-url-or- field--type-link field--label-hidden field__item"><a href="https://www.pathml.org">PathML website</a></div> <div class="field field--name-field-fast-find-service-link field--type-entity-reference field--label-hidden field__item"><a href="/taxonomy/term/8" hreflang="en">Technical Support</a></div> Sat, 01 Jun 2024 23:32:50 +0000 biodata 202 at https://informatics-analytics.dfci.harvard.edu GPT4DFCI https://informatics-analytics.dfci.harvard.edu/gpt4dfci <span class="field field--name-title field--type-string field--label-hidden">GPT4DFCI</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/1" hreflang="en">DFCI</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/155" typeof="schema:Person" property="schema:name" datatype="">biodata</span></span> <span class="field field--name-created field--type-created field--label-hidden">Wed, 03/27/2024 - 19:49</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>GPT4DFCI, a private, secure, HIPAA-compliant generative AI tool based on GPT and o1 models, is now available to Dana-Farber&nbsp;workforce members to try out for work purposes, excluding clinical care.</p> <p><strong>To request access:</strong></p> <ol> <li>If working remotely, be sure you're connected to VPN.</li> <li>Visit the&nbsp;<a href="https://dfciservicerequest.dfci.harvard.edu/?RelayState=GPT4DFCI" rel=" noopener" target="_blank">Informatics &amp; Analytics GPT4DFCI sign-up page</a>.</li> <li>Log in with your MGB username and password.</li> <li>Complete and submit the ticket.</li> <li>Once your access is granted, visit <a href="https://gpt4dfci.dfci.harvard.edu" rel=" noopener" target="_blank">https://gpt4dfci.dfci.harvard.edu</a>&nbsp;</li> </ol> <p>Please review Dana-Farber’s&nbsp;<a href="https://dfcipolicies.ellucid.com/documents/view/9473" rel=" noopener" target="_blank"><strong>new policy on acceptable use of generative AI</strong></a>. Workforce members are required to use generative AI systems in a manner that maintains the protection of protected health information (PHI), personally identifiable information (PII), and other confidential information. It also must be used in a manner that maintains the integrity required for scientific analysis as well as generation of scientific content such as text, images, graphics, and figures.</p> <p><em>Please remember,&nbsp;publicly available AI tools can pose significant privacy and security risks. For this reason, only Dana-Farber-approved AI tools can be used for work purposes.</em></p> <p>Do you want to discuss an idea for a custom GPT? Would you like API access? <a href="https://informatics-analytics.dfci.harvard.edu/groups/artificial-intelligence-operations-data-science-services">Get in touch</a>.</p> <p><strong>More information: </strong><a href="https://www.dana-farber.org/newsroom/news-releases/2024/private-and-secure-generative-ai-tool-supports-operations-and-research-at-dana-farber">GPT4DFCI Press Release</a>.</p> </div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/30" hreflang="en">Analytics users</a></div> <div class="field__item"><a href="/taxonomy/term/20" hreflang="en">Basic researchers</a></div> <div class="field__item"><a href="/taxonomy/term/17" hreflang="en">Belfer Office for Dana-Farber Innovations (BODFI)</a></div> <div class="field__item"><a href="/taxonomy/term/14" hreflang="en">Budget office</a></div> <div class="field__item"><a href="/taxonomy/term/11" hreflang="en">Clinical researchers</a></div> <div class="field__item"><a href="/taxonomy/term/13" hreflang="en">Clinical trial administration</a></div> <div class="field__item"><a href="/taxonomy/term/18" hreflang="en">Office of General Council</a></div> <div class="field__item"><a href="/taxonomy/term/15" hreflang="en">Pharmacy</a></div> <div class="field__item"><a href="/taxonomy/term/16" hreflang="en">Research administrators</a></div> <div class="field__item"><a href="/taxonomy/term/12" hreflang="en">Research staff</a></div> </div> <div class="field field--name-field-fast-find-service-link field--type-entity-reference field--label-hidden field__item"><a href="/taxonomy/term/8" hreflang="en">Technical Support</a></div> Wed, 27 Mar 2024 23:49:12 +0000 biodata 200 at https://informatics-analytics.dfci.harvard.edu Request a report/dashboard https://informatics-analytics.dfci.harvard.edu/request-reportdashboard <span class="field field--name-title field--type-string field--label-hidden">Request a report/dashboard</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/1" hreflang="en">DFCI</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/7" typeof="schema:Person" property="schema:name" datatype="">KRT9</span></span> <span class="field field--name-created field--type-created field--label-hidden">Fri, 09/27/2019 - 08:59</span> <div class="clearfix text-formatted field field--name-field-brief-description field--type-text field--label-hidden field__item">Request an ad hoc report/data for analysis</div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>You can use this form to request reports/dashboards and data for all your analytics requests.</p> <p>Team support email: <a href="mailto:COBA_Support@dfci.harvard.edu">COBA_Support@dfci.harvard.edu</a><br /> <strong>To initiate a new report/dashboard, please fill out</strong>: <a href="https://wiki.dfci.harvard.edu:8443/display/CPT/Report+Request+Form" target="_blank">Request Operational Report, Dashboard</a></p> </div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/30" hreflang="en">Analytics users</a></div> </div> Fri, 27 Sep 2019 12:59:18 +0000 KRT9 77 at https://informatics-analytics.dfci.harvard.edu Request Tableau® access https://informatics-analytics.dfci.harvard.edu/request-tableaur-access <span class="field field--name-title field--type-string field--label-hidden">Request Tableau® access</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/1" hreflang="en">DFCI</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/7" typeof="schema:Person" property="schema:name" datatype="">KRT9</span></span> <span class="field field--name-created field--type-created field--label-hidden">Fri, 09/27/2019 - 08:57</span> <div class="clearfix text-formatted field field--name-field-brief-description field--type-text field--label-hidden field__item">Request access to the Tableau® server for viewing a report/dashboard</div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>Team Support Email: <a href="mailto:COBA_Support@dfci.harvard.edu">COBA_Support@dfci.harvard.edu</a><br /> To request access, please fill out: <a href="https://wiki.dfci.harvard.edu:8443/display/CPT/Access+Request+Form" target="_blank">Access Request Form</a></p> </div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/30" hreflang="en">Analytics users</a></div> </div> Fri, 27 Sep 2019 12:57:19 +0000 KRT9 76 at https://informatics-analytics.dfci.harvard.edu Data acquisition & exploration https://informatics-analytics.dfci.harvard.edu/data-acquisition-exploration <span class="field field--name-title field--type-string field--label-hidden">Data acquisition &amp; exploration</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/1" hreflang="en">DFCI</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/7" typeof="schema:Person" property="schema:name" datatype="">KRT9</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 08/08/2019 - 09:17</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>COBA facilitates data acquisition and definition of data structures, in partnership with other teams across Informatics and DFCI. The <a href="/groups/enterprise-data-warehouse">Enterprise Data Warehouse</a> team and COBA have made joint efforts to link data from Peoplesoft, EPIC, Info-ed, OnCore, and more into integrated and easily queried views for DFCI users.<br /> <br /> COBA routinely inventories the available data to understand which metrics are available in EPIC, DataSteward, EPSi, PeopleSoft, etc., and determine metrics that can be calculated by manipulating existing fields.</p> </div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/30" hreflang="en">Analytics users</a></div> </div> <div class="field field--name-field-access-and-support-url-or- field--type-link field--label-hidden field__item"><a href="mailto:COBA_Support@dfci.harvard.edu">COBA Support email</a></div> Thu, 08 Aug 2019 13:17:40 +0000 KRT9 35 at https://informatics-analytics.dfci.harvard.edu Reporting & dashboarding https://informatics-analytics.dfci.harvard.edu/reporting-dashboarding <span class="field field--name-title field--type-string field--label-hidden">Reporting &amp; dashboarding</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/1" hreflang="en">DFCI</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/7" typeof="schema:Person" property="schema:name" datatype="">KRT9</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 08/08/2019 - 09:16</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>While both reports and dashboards present statistics, charts, and figures tailored to the needs of the user, they differ in their format. Reports are built as static PDFs and Excel spreadsheets, and are ideal for focused, single-use tasks with a shorter turnaround time.<br /> <br /> Dashboards are a dynamic, interactive service, built in the intuitive but powerful business intelligence package Tableau<sup>®</sup>. Dashboards are published to a server, where they are accessible by specified users from anywhere within the Dana-Farber network. They are equipped with customizable filters and drilling options that can be adjusted by the user and reconfigured by the department’s business steward, drawing from data sources that can be configured to update as frequently as once per night.&nbsp;<br /> <br /> Both dashboards and reports can be used to inform day-to-day operations, assist in the completion of internal and external reporting requirements, and evaluate the effectiveness of operational policy.<br /> <br /> <strong>Note: This form is not for research.&nbsp;</strong>If this request is research-related or in any way involves IRB approval, this is NOT the correct form. Please view&nbsp;<a href="/services/research-data-access">Research Data Requests</a>.</p> </div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/30" hreflang="en">Analytics users</a></div> </div> <div class="field field--name-field-access-and-support-url-or- field--type-link field--label-hidden field__item"><a href="https://wiki.dfci.harvard.edu:8443/display/CPT/Report+Request+Form">Request Operational Report, Dashboard</a></div> Thu, 08 Aug 2019 13:16:13 +0000 KRT9 34 at https://informatics-analytics.dfci.harvard.edu Analytics assessment & consultation https://informatics-analytics.dfci.harvard.edu/analytics-assessment-consultation <span class="field field--name-title field--type-string field--label-hidden">Analytics assessment &amp; consultation</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/1" hreflang="en">DFCI</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/7" typeof="schema:Person" property="schema:name" datatype="">KRT9</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 08/08/2019 - 09:13</span> <div class="clearfix text-formatted field field--name-field-brief-description field--type-text field--label-hidden field__item">Workflow optimization, reporting and visualization best practices, software and business intelligence tools training</div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>Within DFCI, and at a state and federal level, the demand for data-driven care is growing exponentially. While the possibility for analytics infrastructure to support efficient, equitable, and high-quality care is exciting, incomplete or inconsistent implementation can create confusion and fatigue.<br /> <br /> COBA is here to support any DFCI initiative that promotes data acquisition and analytics. This includes, but is not limited to, workflow optimization, reporting and visualization best practices, and software and business intelligence tools trainings (including Tableau<sup>®</sup> and Confluence).<br /> <br /> COBA’s workflow optimization service audits the user’s process from data entry to interpretation and presentation, to ensure that all processes are robust, efficient, and unbiased.</p> </div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/30" hreflang="en">Analytics users</a></div> </div> <div class="field field--name-field-access-and-support-url-or- field--type-link field--label-hidden field__item"><a href="mailto:COBA_Support@dfci.harvard.edu">COBA Support email</a></div> Thu, 08 Aug 2019 13:13:08 +0000 KRT9 33 at https://informatics-analytics.dfci.harvard.edu