We have received several inquiries about depositing RNA-seq data generated by WashU’s Genome Technology Access Center (GTAC) into the Gene Expression Omnibus (GEO) repository managed by the National Center for Biotechnology Information (NCBI). As a result, it is a good time to write a blog article providing guidance on this issue for researchers on campus. [Read more]
In recent years, there has been exponential growth in the use of machine learning (ML) in the life sciences, fueled by increased access to powerful hardware (e.g., GPUs) and high-quality FAIR biodata enabled by the open science movement. One standout example is AlphaFold, which uses ML to predict protein structure from genetic sequences, a breakthrough [Read more]
In the first two parts of this blog series, I introduced the main player in the proteomics data repository ecosystem, the ProteomeXchange (PX) Consortium. Outside of the PX Consortium, there are an additional handful of repositories holding proteomics data. These additional repositories serve special cases or certain scientific communities, but it may be useful for [Read more]
In the first part of this blog series, I provided an overview of the ProteomeXChange (PX) Consortium and introduced its most important member – the PRIDE Database. I also introduced ProteomeCentral, the common portal providing the ability to browse and search all of the public datasets within the PX Consortium member repositories. Here in the [Read more]
Introduction Proteomics, the large-scale study of proteomes, is a highly valuable tool in biomedical research, but because most proteomics approaches are based on mass spectrometry (MS), the analytical chemistry nature can be a barrier to some biologists and physician-scientists. In this series of three blog articles, I would like to introduce MS-based proteomics data by [Read more]
The National Institutes of Health (NIH) requires a Data Management and Sharing Plan (DMSP) in all competing applications that generate scientific data. A DMSP should cover six key elements as outlined in NOT-OD-21-014. While not required, using a DMSP template helps researchers address all six elements and sub-elements required by the NIH DMS policy. The [Read more]
Earlier this year, the National Library of Medicine (NLM) announced the launch of the beta version of a new online tool called the Dataset Catalog. This tool is intended to be the “PubMed of datasets” to help users search, find and retrieve datasets in multiple repositories through a single, user-friendly interface. Dataset Catalog beta currently [Read more]
Are you frustrated by incomplete methods in publications that lack critical details? Are you seeking a simple solution to document comprehensive step-by-step protocols, complete with information on reagents and equipment, and a dedicated space to note any protocol deviations? In research settings, reproducible experimental methods are of utmost importance. Fortunately, protocols.io offers a solution where [Read more]
In August 2022, the White House Office of Science & Technology Policy (OSTP) issued a memo: Ensuring Free, Immediate, and Equitable Access to Federally Funded Research (OSTP 2022 Nelson Memo), that directs federal agencies to update their public access policies per OSTP 2013 Holdren Memo. The policies pertain to publications, scientific data underlying publications, and [Read more]
Are you working on a Data Management and Sharing (DMS) Plan for your NIH grant application under the 2023 NIH DMS policy (NOT-OD-21-013) and curious about the evaluation metric? Check out NIH’s ongoing pilot with DMS Plan templates Alpha and Bravo. The Federal Demonstration Partnership (FDP) NIH DMS Pilot, launched on March 1, 2023, is [Read more]