Molecular Informatics Core
Brown/Lifespan Center for Clinical Cancer Informatics and Data Science URI Road Show
“Science” Genuine images in 2024
Molecular Informatics Core (MIC)
As we ring in the new year, this is a good time for the MIC to assess the state of the rapidly changing fields of bioinformatics and biomedical data science. Our goal is to stay up to date on the newest technologies and methodologies and to maintain and build our regional network of core facilities to ensure that our users have access to whatever resources they need to achieve their research goals.
First, we are happy to announce a collaboration between the MIC, the CRCF, and the URI College of Pharmacy (COP) to advance the College’s proteomics capabilities. Over the last several years RI-INBRE and the COP have made investments in new mass spectrometry technology for proteomics managed by CRCF Director Ang Cai and COP Research Scientist Chang Liu. The three of us are now working together and with regional partners to establish best practices and standardized workflows for proteomics analyses at URI. We wat these workflows to cover every step of the proteomics process, including establishment of data management and sharing plans, experimental design and power analysis, and data acquisition, analysis, and visualization. We welcome any input from you on this process.
Second, we are expanding the scope of our services to single cell and spatial omics technologies. Dr. Alan Rothman recently housed his 10X Genomics Chromium Controller to the CRCF and we are planning to upgrade that machine to the newest Chromium X model in the very near future. We are also talking with several vendors who operate in the spatial omics sector about their services, and we will explore purchasing these machines based on demand and resources. Please let us know if you are interested in single cell and/or spatial omics work and how these resources might help you.
Finally, we are focusing more efforts on cloud computing technologies, particularly the Terra ecosystem maintained by the Broad Institute. Specifically, we are working with the All of Us platform which allows for large-scale cohort studies using a variety of data types (including wearable devices, clinical data, and genomic data). We are currently working with Dr. Gabrielle Papale at Salve Regina University and Dr. Xuerong Wen at URI on a genome-wide association study using the All of Us platform. From this work we will establish workflows and best practices for these platforms so that other researchers can make us of them.
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Brown/Lifespan Center for Clinical Cancer Informatics and Data Science URI Road Show
On December 8, 2023, RI-INBRE hosted the Brown/Lifespan Center for Clinical Cancer Informatics and Data Science (CCIDS) Road Show and the Bioinformatics Journal Club at Avedisian Hall. The CCIDS is interested in collaborating with URI faculty working in the areas of experimental cancer research, cancer informatics, and cancer-related health outcomes research.
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“Science” Genuine images in 2024
The journal Science announced that its six journals will begin using the AI tool Proofig to identify cases of fraudulently generated images, with a particular interest on easily manipulated images like western blots, microscopy images, and flow cytometry. Proofig will be run after a revised manuscript has been submitted and if images are flagged, the editors will reach out to the authors for justification. If this happens to you, do not take it as an accusation of fraud. AI tools have a high false positive rate and Science has found that in most of the flagged cases prior to full implementation of this policy, the authors were able to justify the images. In many cases, the issue was inadvertent and not intended to be fraudulent. This policy will likely be expanded to other journals and probably funding agencies in the near future. Read more
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