Biology subjects

Martins Ratamero, E.

Publications and source records attributed to Martins Ratamero, E..

3 recordsLinked to original sources

bioRxiv2023

Easing OMERO adoption with ezomero

Many research laboratories need to manage, process, and analyze the increasingly large volumes and complexity of data being produced by state-of-the-art bioimaging platforms. OMERO is a popular open-source client-server application that provides a unified interface for managing and working with bioimages and their associated measurements and metadata. Integrating OMERO into analysis pipelines, such as those developed around the scientific Python ecosystem, will thus be a common pattern across the field of bioimaging. While OMERO has a powerful Python API, it provides minimal abstraction from the underlying OMERO object model and associated methods, which represent more complexity than most users are interested in for the context of an analysis script. We introduce ezomero, which was designed to provide a convenience layer on top of existing OMERO APIs and return data types that are either Python primitive or commonly used in scientific Python. Ezomero has minimal dependencies in addition to the OMERO Python library itself and is installable directly from PyPI. Here, we provide an overview of ezomero as well as several vignettes to illustrate how it can be used to accelerate discovery.

bioinformatics↗

bioRxiv2019

Calculating the maximum capacity of intracellular transport vesicles

In eukaryotic cells, vesicles transport protein cargo to various destinations in the cell. As part of an effort to count the number of cargo molecules in vesicles in cells, we asked a simple question: what is the maximum number of cargo molecules that can be packed into a vesicle? The answer to this question lies in the Tammes Problem, which seeks to determine the packing of circles on a spherical surface. The solution to this problem depends on the sizes of the vesicle and the cargo. We present here the computational results that determine the maximum theoretical capacity of a range of biologically relevant cargo in a variety of meaningful vesicle sizes. Our results could be generalized in order to describe an equation that allows the calculation of the approximate maximum capacity of any vesicle, whatever the size; provided that the size and geometry of the cargo is known.

cell biology↗

bioRxiv2017

Touching proteins with virtual bare hands: how to visualize protein-drug complexes and their dynamics in virtual reality

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful features. A more precise visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). In this work, we present a freely available software pipeline for visualising protein structures through VR. New customer hardware, such as the HTC VO_SCPCAPIVEC_SCPCAP and the OO_SCPCAPCULUSC_SCPCAP RO_SCPCAPIFTC_SCPCAP utilized in this study, are available at reasonable prices. Moreover, we have combined VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-lead drug design by exposing molecular interactions that might be hidden in the less informative static models.

bioinformatics↗