The void between preclinical testing and clinical trials of drugs reveals a crucial roadblock to efficient drug discovery. This plan defines an apporach to bioengineer structurally representative human tissues in vitro using the power of outstanding international academic collaborations.
collaboration
Natural killer (NK) cells are cytotoxic immune cells that play an important role in the defense against cancer.
https://mrna.creative-biolabs.com/custom-natual-killer-cell-reprogramming-by-mrna.htm
The void between preclinical testing and clinical trials of drugs reveals a crucial roadblock to efficient drug discovery. This plan defines an apporach to bioengineer structurally representative human tissues in vitro using the power of outstanding international academic collaborations.
collaboration
Natural killer (NK) cells are cytotoxic immune cells that play an important role in the defense against cancer.
https://mrna.creative-biolabs.com/custom-natual-killer-cell-reprogramming-by-mrna.htm
Nanoparticle Drug Delivery Systems for Cancer TreatmentAranca
The engineered nanoparticles are effectively used for cancer treatment due to their targeted drug delivery approach. Download the Aranca report on Technology and Patent Research for current research trends and developments.
Growth Kinetics of 2- and 3-D Cell Models as Influenced by the MicroenvironmentТатьяна Гергелюк
The noncontact cocultivation system was developed for the study of the paracrine interactions
between MCF-7 (breast carcinoma cells) and MT-4 (a line of human T-cell leukemia). Viability and proliferation
rates were determined in the adhesion and suspension fractions of MCF-7 cells sampled from two model
systems: monolayer culture and multicellular tumor spheroids (MTS). Cocultivation with MT-4 reduced the
number of MCF-7 cells in the adhesion fraction and had no effect upon the suspension fraction, despite an
increase in the total population of MCF-7 cells. The two model systems displayed a substantial difference in
cell viability, alone and in the presence of MT-4 cells – the fraction of viable cells in the monolayers was greater
than in the spheroids. It is suggested that cocultivation with MT-4 stimulates proliferation of MCF-7 cells via
a paracrine mechanism, reduces adhesion to the substrate, and leads to MTS formation.
Molecular imaging has revolutionized our perceptions of imaging. This high impact field is finding transformative applications in the understanding, detection, and treatment of nearly all diseases.
The field of molecular imaging is a an exciting fusion and integration of many different disciplines including molecular biology, chemistry and probe design, imaging technologies, visualization, and image analysis, that are focused on understanding, detecting, and treating oncological, neurological, cardiovascular, inflammatory, metabolic, and infectious diseases. Based on their strengths, different imaging modalities provide different but equally valuable information that can be integrated in advancing our understanding of these diseases.
As the era of ‘omics’ progresses towards personalized medicine, the field of molecular imaging is finding multiple uses in noninvasive characterization of the molecular features of diseases and their impact on function. In complex diseases such as cancer, with its tremendous genetic diversity, it is becoming increasingly important to develop molecularly-targeted treatment strategies that combine detection with treatment.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.2- Next Generation Sequencing. Technologies and Applications. Part II: NGS Applications I.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Nanoparticle Drug Delivery Systems for Cancer TreatmentAranca
The engineered nanoparticles are effectively used for cancer treatment due to their targeted drug delivery approach. Download the Aranca report on Technology and Patent Research for current research trends and developments.
Growth Kinetics of 2- and 3-D Cell Models as Influenced by the MicroenvironmentТатьяна Гергелюк
The noncontact cocultivation system was developed for the study of the paracrine interactions
between MCF-7 (breast carcinoma cells) and MT-4 (a line of human T-cell leukemia). Viability and proliferation
rates were determined in the adhesion and suspension fractions of MCF-7 cells sampled from two model
systems: monolayer culture and multicellular tumor spheroids (MTS). Cocultivation with MT-4 reduced the
number of MCF-7 cells in the adhesion fraction and had no effect upon the suspension fraction, despite an
increase in the total population of MCF-7 cells. The two model systems displayed a substantial difference in
cell viability, alone and in the presence of MT-4 cells – the fraction of viable cells in the monolayers was greater
than in the spheroids. It is suggested that cocultivation with MT-4 stimulates proliferation of MCF-7 cells via
a paracrine mechanism, reduces adhesion to the substrate, and leads to MTS formation.
Molecular imaging has revolutionized our perceptions of imaging. This high impact field is finding transformative applications in the understanding, detection, and treatment of nearly all diseases.
The field of molecular imaging is a an exciting fusion and integration of many different disciplines including molecular biology, chemistry and probe design, imaging technologies, visualization, and image analysis, that are focused on understanding, detecting, and treating oncological, neurological, cardiovascular, inflammatory, metabolic, and infectious diseases. Based on their strengths, different imaging modalities provide different but equally valuable information that can be integrated in advancing our understanding of these diseases.
As the era of ‘omics’ progresses towards personalized medicine, the field of molecular imaging is finding multiple uses in noninvasive characterization of the molecular features of diseases and their impact on function. In complex diseases such as cancer, with its tremendous genetic diversity, it is becoming increasingly important to develop molecularly-targeted treatment strategies that combine detection with treatment.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.2- Next Generation Sequencing. Technologies and Applications. Part II: NGS Applications I.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Overview of the commonly used sequencing platforms, bioinformatic search tool...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
Learning, Training, Classification, Common Sense and Exascale ComputingJoel Saltz
In this talk, I will describe work my group has carried out in development of deep learning methods that target semantic segmentation and object identification tasks in terapixel Pathology datasets and for satellite data. I will describe what we have been able to achieve, how this work can generalize to additional types of problems and will outline how exascale computing could be used to transform and integrate our methods and pipelines. I will then go on to outline broad research program in exascale computing and deep learning that promises to identify common deep learning methods for previously disparate large and extreme scale data tasks.
it will help you to understand how the protein microarrays are made, what are the different types and what all purposes they are used for. its very useful ppt
Anticancer drug discovery using multicellular tumor spheroid modelsHasnat Tariq
Cancer, drug discovery, tumor spheroids, organoids, 3D tumor spheroids, 3D scaffold-based models, Scaffold-free models, 3D Scaffolds, Hanging drop, Low adhesion microplate, Magnetic levitation and bio printing, bioprinting, anticancer,, tumor models, Drug screening assays, flow cytometry, expansion microscopy.
Genomic Cytometry: Using Multi-Omic Approaches to Increase Dimensionality in ...Robert (Rob) Salomon
"Genomic Cytometry: Using Multi-Omic Approaches to Increase Dimensionality in Cytometry" was an Invited Tutorial given at the 2019 CYTO conference for the the International Society for the Advancement of Cytometry on the 22nd May 2019. This tutorial was recorded and we expect that it will be converted to a CYTOU webinar in the near future.
This tutorial will begin by explaining why the emerging field of Genomic Cytometry, i.e. the measurement of cells using genomic techniques (e.g. sequencing), in conjunction with more traditional cytometry techniques such as fluorescence, mass and imaging cytometry is becoming a standard tool for biologists looking to unravel complex cellular processes and to develop a deeper understanding of heterogeneity.
We will give a detailed overview of the various technologies that have allowed the emergence of Genomic Cytometry as well as those that continue to push the boundaries of cellular characterisation.
We will then provide a basic overview of the sequencing process such that both research cytometerists and the staff for the cytometry SRL are better equipped to understand the downstream genomic component of Genomic Cytometry.
Finally, we will wrap up the session with case studies that illustrate the power of the genomic cytometry approach and will give a brief outline of where we feel the field needs to go as it matures. We expect attendees will gain a better understanding of 1) the rapidly maturing field of Genomic Cytometry and 2) how Genomic Cytometry should be leveraged into more traditional cytometry workflows.
Accelerating the Delivery of New Treatments for Children with Neuroblastoma 2...Scintica Instrumentation
Neuroblastoma is a tumour arising from anomalies in the development of the sympathic nervous system and still accounts for 13% of all cancer-related death in children due to resistant, relapsing and metastatic diseases. There is an urgent need for the development of new treatment against high-risk relapsed neuroblastoma.
Overview:
Here we will discuss the ICR Paediatric Mouse Hospital approach which integrates more advanced mouse modelling, such as the use of genetically-engineered mouse (GEM) models and patient-derived xenografts to accelerate the discovery and evaluation of novel therapeutic strategies and help shape the clinical trial pipeline priorities for children with high-risk relapsing/refractory neuroblastoma.
We will also highlight the pivotal role of MRI within the Mouse Hospital which includes:
Enhancing and accelerating preclinical trials
Quantitatively inform on tumour phenotype and tumour response to treatment to:
Develop in vivo models that emulate the clinical treatment resistant phenotype using chemotherapy-dose escalation protocol
Characterize tumour spatial heterogeneity and evolution over treatment and guide the pathological and molecular characterization of the resistant phenotype
Finally we will also discuss how the compact, cryogen-free and user-friendly Aspect Imaging M-Series has transformed our way of working within the mouse hospital by providing a shared and easily accessible resource for tumour screening (with minimal onboarding) .
dkNET Webinar: The Human BioMolecular Atlas Program (HuBMAP) 10/14/2022dkNET
Abstract
HuBMAP aims to catalyze the development of an open, global framework for comprehensively mapping the human body at cellular resolution. HuBMAP goals include: (1) Accelerate the development of the next generation of tools and techniques for constructing high resolution spatial tissue maps. (2) Generate foundational 3D tissue atlases. (3) Establish an open data platform. (4) Coordinate and collaborate with other funding agencies, programs, and the biomedical research community. (5) Support projects that demonstrate the value of the resources developed by the program. The HuBMAP Portal can be found at https://portal.hubmapconsortium.org and the Visible Human MOOC describes the compilation and coverage of HuBMAP data, demonstrates new single-cell analysis and mapping techniques, and introduces major features of the HuBMAP portal.
The top 3 key questions that HuBMAP can answer:
1. What assay types are best to map the human body in 3D and across scales?
2. What Common Coordinate System (CCF) is best to construct the Human Reference Atlas?
3. How can others help construct and/or use the Human Reference Atlas?
Presenters:
Katy Börner, PhD, Victor H. Yngve Distinguished Professor of Engineering and Information Science, Department of Intelligent Systems Engineering and Information Science, Indiana University
Jeffrey Spraggins, PhD, Assistant Professor, Department of Cell and Developmental Biology, Vanderbilt University
Upcoming webinars schedule: https://dknet.org/about/webinar
Molecular Biology research evolves through the development of the technologies used for carrying them out. It is not possible to research on a large number of genes using traditional methods
Similar to CMSO Minimal reporting requirements (20)
Talk given at the Data Visualisation and the Future of Academic Publishing event. https://www.eventbrite.com/e/data-visualisation-and-the-future-of-academic-publishing-tickets-25372801733?password=dataviz
From peer-reviewed to peer-reproduced: a role for research objects in scholar...Alejandra Gonzalez-Beltran
The reproducibility of science in the digital age is attracting a lot of attention and concerns from the scientific community, where studies have shown the inability to reproduce results due to a variety of reasons, ranging from unavailability of the data to lack of proper descriptions of the experimental steps.
Multiple research object models have been proposed to describe different aspects of the research process. Investigation/Study/Assay (ISA) is a widely used general-purpose metadata tracking framework with an associated suite of open-source software, which offers a rich description of the experiment’s hypotheses and design, investigators involved, experimental factors, protocols applied. The information is organised in a three-level hierarchy where ’Investigation’ provides the project context for a ’Study’ (a research question), which itself contains one or more ’Assays’ (taking analytical measurements and key data processing and analysis steps). Nanopublication (NP) is a research object model which enables specific scientific assertions, such as the conclusions of an experiment, to be annotated with supporting evidence, published and cited. Lastly, the Research Object (RO) is a model that enables the aggregation of the digital resources contributing to findings of computational research, including results, data and software, as citable compound digital objects.
For computational reproducibility, platforms such as Taverna and Galaxy are popular and efficient ways to represent the data analysis steps in the form of reusable workflows, where the data transformations can be specified and executed in an automatic way.
In this presentation, we will address the question of whether such research object models and workflow representation frameworks can be used to assist in the peer review process, by facilitating evaluation of the accuracy of the information provided by scientific articles with respect to their repeatability.
Our case study is based on an article on a genome assembler algorithm published in GigaScience, but due to the proven use of the respective research object models in their respective communities, we argue that the combination of models and workflow system will improve the scholarly publishing process, making science peer-reproduced.
Increased access to the data generated is fuelling increased consumption and accelerating the cycle of discovery. But the successful integration and re-use of heterogeneous data from multiple providers and scientific domains is a major challenge within academia and industry, often due to incomplete description of the study details or metadata about the study. Using the BioSharing, ISA Commons and the STATistics Ontology (STATO) projects as exemplar community efforts, in this breakout session we will discuss the evolving portfolio of community-based standards and methods for structuring and curating datasets, from experimental descriptions to the results of analysis.
http://www.methodsinecologyandevolution.org/view/0/events.html#Data_workshop
Seminario en CIFASIS, Rosario, Argentina - Seminar in CIFASIS, Rosario, Argen...Alejandra Gonzalez-Beltran
La biología experimental se ha convertido en una ciencia intensiva en datos, gracias a los avances en las tecnologías de adquisición de señales digitales y biosensores. La disponibilidad de los datos es fundamental para la transparencia del proceso científico: para poder reproducir los resultados y también para la reutilización de los datos en estudios futuros. Esta charla explorará distintas herramientas de software que facilitan el proceso de generación de metadatos para mejorar la calidad, el reporte, la publicación y la revisión de datos, con énfasis en aplicaciones biomédicas.
Slides introducing the session on 'Big data in healthcare' at the Brazil-UK Frontiers of Engineering symposium held at Jarinu, Sao Paulo, Brazil - 6-8 November 2014.
Metagenomic Data Provenance and Management using the ISA infrastructure --- o...Alejandra Gonzalez-Beltran
Metagenomic Data Provenance and Management using the ISA infrastructure - overview, implementation patterns & software tools
Slides presented at EBI Metagenomics Bioinformatics course: http://www.ebi.ac.uk/training/course/metagenomics2014
This talk explores how principles derived from experimental design practice, data and computational models can greatly enhance data quality, data generation, data reporting, data publication and data review.
Quantitative Data AnalysisReliability Analysis (Cronbach Alpha) Common Method...2023240532
Quantitative data Analysis
Overview
Reliability Analysis (Cronbach Alpha)
Common Method Bias (Harman Single Factor Test)
Frequency Analysis (Demographic)
Descriptive Analysis
Adjusting primitives for graph : SHORT REPORT / NOTESSubhajit Sahu
Graph algorithms, like PageRank Compressed Sparse Row (CSR) is an adjacency-list based graph representation that is
Multiply with different modes (map)
1. Performance of sequential execution based vs OpenMP based vector multiply.
2. Comparing various launch configs for CUDA based vector multiply.
Sum with different storage types (reduce)
1. Performance of vector element sum using float vs bfloat16 as the storage type.
Sum with different modes (reduce)
1. Performance of sequential execution based vs OpenMP based vector element sum.
2. Performance of memcpy vs in-place based CUDA based vector element sum.
3. Comparing various launch configs for CUDA based vector element sum (memcpy).
4. Comparing various launch configs for CUDA based vector element sum (in-place).
Sum with in-place strategies of CUDA mode (reduce)
1. Comparing various launch configs for CUDA based vector element sum (in-place).
The Building Blocks of QuestDB, a Time Series Databasejavier ramirez
Talk Delivered at Valencia Codes Meetup 2024-06.
Traditionally, databases have treated timestamps just as another data type. However, when performing real-time analytics, timestamps should be first class citizens and we need rich time semantics to get the most out of our data. We also need to deal with ever growing datasets while keeping performant, which is as fun as it sounds.
It is no wonder time-series databases are now more popular than ever before. Join me in this session to learn about the internal architecture and building blocks of QuestDB, an open source time-series database designed for speed. We will also review a history of some of the changes we have gone over the past two years to deal with late and unordered data, non-blocking writes, read-replicas, or faster batch ingestion.
1. Minimal reporting
requirements for
cell migration (WG1)
Alejandra Gonzalez-Beltran
Oxford e-Research Centre, University of Oxford
@alegonbel
CSMO Workshop, 19th June 2017, Essen, Germany
2. Working Group Objectives
● Formulation of a reporting guideline for Cell Migration experiments
(MIACME) supporting the requirements to make data produced in such
experiments FAIR (Findable Accessible Interoperable and Reusable)
● Reach agreement from the community on the minimal descriptors (and
extended descriptors) required to understand, interpret, evaluate, replicate
and disseminate cell migration experiments
● Use MIACME to promote data access, data discovery, data preservation
and to maximise data re-use and repurpose through efficient annotation for
long term archiving
● Ultimately, enable reproducibility of cell migration experiments
3. MIACME development
● Gradient of information (data discovery/access/preservation to understand,
interpret, evaluate, re-use, repurpose, replicate, reproduce)
● Iterative process: (design → test → refine → evaluate) cycle
● “Minimal” set of descriptors
○ Strike the right balance between number of descriptors and the objectives for collecting them
○ “Minimal” is dependent on experiment type
■ Consider core set of descriptors and extensions, if necessary
○ “Optimal” set of descriptors
● Community-led process
○ Community consensus is key to agree on a standard way of reporting cell migration
experiments
14. MIACME v0.2 - Experimental setup
Assay
type
Interference
Microenv
substrate
Microenv
tissue Cell type Medium
Experimental setup
single-cell
migration,
collective cell
migration,
developmental
assay, immune
response,
chemotaxic,
microfluidic,
wound-healing,
spheroid
RNAi, gene
construct,
chemicals, serum,
substrate
stiffness
-------------------------
specific protein
glass, plastic,
ECM, gel
-------------------------
Collagen,
fibronectin
mouse,
dermis,
Zebrafish
embryo
cell line,
primary cell,
endogenous
cell
EGF, HGF
one or the other
15. MIACME v0.2 - Imaging condition
Imaging condition
Imaging
modality
confocal
microscopy,
spinning disk,
wide-field,
multi-photon,
light-sheet,
super-resolution,
phase-contrast
Temporal
resolution
end-point,
time-lapse
Duration and
frequency
Objective
Channel
readout 1..n
36 hours, 10
minutes
20x, oil
conditional on
time-lapse
Specific
protein/subcellular
compartment,
traction force
beads, ratio (FRET),
cell body/bodies
-----------------------------
-
antibody,
FP-tagged, dye
16. MIACME v0.2 - Data
Data (1..n)
Raw images
YES or NO
Total number
of images
conditional
on YES
250
Processed
images
Extracted
features
trajectories (x, y, t),
derived quantities
like cell speed,
persistence of
motion, shape
features (cell area,
cell solidity, cell
perimeter…)
filtered images,
deconvoluted
images, masked
images, images
with tracks overlay,
traction flow, PIV
flow fields
23. Roadmap
MIACME v0.2 has focused on identifying the main descriptors. In the next steps,
we will:
● produce more examples of MIACME-compliant descriptions of different types
of cell migration experiments for evaluation
● include further requirements related to semantic artifacts and other external
resources
● consider relationship/alignment with other resources, e.g. MIACA - Minimum
Information About a Cellular Assay
● release new versions of the MIACME checklist after incorporating the
feedback received
24. Workshop Work Plan Proposal
● Revision of MIACME v0.2
○ Provide comments on current descriptors and suggestions for additions / modifications
○ Has the simplification reached the right balance?
● Collect publications/experiments/datasets to be described with MIACME
○ Work in on own publication/dataset
○ Peer assessment
● Analysis of groups’ experimental setups
● Create task forces to deal with specific experiment types
● Work on automatic extraction of some MIACME metadata
○ e.g. objective and temporal resolution
● Interactions with other working groups to consider MIACME in relation to
○ Semantic artifacts and other external resources
○ Formats and APIs