Presentation made by Andy Jarvis in the workshop on Adapting agriculture to climate change: The role of crop wild relatives, in Bellagio, Italy, 7th-9th September 2010.
Practical interoperability across semantic stores of data for ecological, tax...Cyndy Parr
Presented at the Biodiversity Information Standards (Taxonomic Databases Working Group) 2013 meeting in Florence, Italy on 31 October 2013. Essentially, an introduction to aspects of the back end of the new trait repository of Encyclopedia of Life.
SeraCare provides reference materials and tools to address challenges in precision medicine and next generation sequencing (NGS)-based assays. Their highly multiplexed reference materials allow labs to identify assay variability and design reference materials in silico. Their biomimetic materials mimic patient samples with equivalent performance and enhanced stability. Engineered cell lines mimic rare patient-derived tumor types and variants. Their products and technologies help with development, validation, production, and reporting for a variety of NGS-based assays including tumor profiling, circulating tumor and fetal DNA, and infectious and inherited disease assays. They provide full-process reference materials in various formats including FFPE tissues, synthetic plasma, and purified DNA produced using digital PCR for high accuracy.
The document discusses a collaboration between researchers from Drexel University, UCSF, and Indiana University aimed at accelerating drug discovery for malaria. The collaboration uses an open science and collaborative drug discovery approach, sharing research over blogs, wikis, and other online platforms. Specifically, the collaboration links synthetic chemistry from Drexel, malaria biology and screening from UCSF, and computational docking from Indiana University to filter a library of compounds for testing against malaria. The researchers have shared screening data and characterized compounds in online databases to make their findings openly accessible.
4th International Conference and Exhibition on Analytical and Bioanalytical Techniques, will be organized around the theme "Showcasing the Contemporary Approaches in Analytical & Bioanalytical Techniques."
The Biodiversity Heritage Library (BHL) is a digital library that aims to make biodiversity literature accessible. It partners with museums, botanical gardens, and university libraries to digitize their collections. The BHL uses various technologies like the Internet Archive for scanning and storage, and provides tools like subject headings, maps, and name finding services to help users discover relevant literature. It plans to migrate to the Fedora platform and expand to include more nodes internationally.
Castor is an oilseed plant which is earning attention on researchers in recent days. Because of this, the gemplasms of ancient varieties were now recovered and grown in trial fields for getting genetically superior variety.
As a result, in Castor and Tapioca research station there a variety named YRCH (Yethapur Ricinus Communis Hybrid) with all desired traits which are essential for a plant both phenotypically and genetically was developed.
The Human Cell Atlas Data Coordination PlatformLaura Clarke
This presentation gives a brief summary of the Human Cell Atlas project and describes the data coordination platform which is being built to support it.
Practical interoperability across semantic stores of data for ecological, tax...Cyndy Parr
Presented at the Biodiversity Information Standards (Taxonomic Databases Working Group) 2013 meeting in Florence, Italy on 31 October 2013. Essentially, an introduction to aspects of the back end of the new trait repository of Encyclopedia of Life.
SeraCare provides reference materials and tools to address challenges in precision medicine and next generation sequencing (NGS)-based assays. Their highly multiplexed reference materials allow labs to identify assay variability and design reference materials in silico. Their biomimetic materials mimic patient samples with equivalent performance and enhanced stability. Engineered cell lines mimic rare patient-derived tumor types and variants. Their products and technologies help with development, validation, production, and reporting for a variety of NGS-based assays including tumor profiling, circulating tumor and fetal DNA, and infectious and inherited disease assays. They provide full-process reference materials in various formats including FFPE tissues, synthetic plasma, and purified DNA produced using digital PCR for high accuracy.
The document discusses a collaboration between researchers from Drexel University, UCSF, and Indiana University aimed at accelerating drug discovery for malaria. The collaboration uses an open science and collaborative drug discovery approach, sharing research over blogs, wikis, and other online platforms. Specifically, the collaboration links synthetic chemistry from Drexel, malaria biology and screening from UCSF, and computational docking from Indiana University to filter a library of compounds for testing against malaria. The researchers have shared screening data and characterized compounds in online databases to make their findings openly accessible.
4th International Conference and Exhibition on Analytical and Bioanalytical Techniques, will be organized around the theme "Showcasing the Contemporary Approaches in Analytical & Bioanalytical Techniques."
The Biodiversity Heritage Library (BHL) is a digital library that aims to make biodiversity literature accessible. It partners with museums, botanical gardens, and university libraries to digitize their collections. The BHL uses various technologies like the Internet Archive for scanning and storage, and provides tools like subject headings, maps, and name finding services to help users discover relevant literature. It plans to migrate to the Fedora platform and expand to include more nodes internationally.
Castor is an oilseed plant which is earning attention on researchers in recent days. Because of this, the gemplasms of ancient varieties were now recovered and grown in trial fields for getting genetically superior variety.
As a result, in Castor and Tapioca research station there a variety named YRCH (Yethapur Ricinus Communis Hybrid) with all desired traits which are essential for a plant both phenotypically and genetically was developed.
The Human Cell Atlas Data Coordination PlatformLaura Clarke
This presentation gives a brief summary of the Human Cell Atlas project and describes the data coordination platform which is being built to support it.
Biodiversity informatics and the agricultural data landscapeCyndy Parr
Introductory talk of a symposium on Agrobiodiversity informatics at the 2016 annual meeting of the Biodiversity Information Standards. Begins with an overview of the symposium and its speakers, and then launches into my talk.
A state-of-the-art biorepository: Challenges and opportunitiesILRI
Presentation by Absolomon Kihara and Steve Kemp at the third Medical and Veterinary Virus Research Symposium (MVVR-3), Nairobi, Kenya, 17 October 2014.
Azizi biorepository: Challenges and opportunitiesILRI
Presentation by Absolomon Kihara and Steve Kemp at an ILRI seminar on managing biological samples held at the ILRI Nairobi campus on 10 September 2013.
Presentation by Simon Mayo at the KikForum
Abstract:
As part of the CATE project we are developing keys in Lucid 3 to the genera of Araceae, and to the genus Anthurium (ca. 800spp.), Arum and Philodendron. The key to Arum is already online. These keys will be incorporated into a web-based taxonomic revision of the Araceae family as the plant model group for the project. Anthurium presents a particular challenge as it is a very large and difficult genus, within which it is currently nearly impossible for non-specialists to determine plants to species. We hope the key will go some way to solving this problem.
Large Scale computing with medical metabolic phenotyping dataChristoph Steinbeck
This document discusses large scale computing with medical metabolic phenotyping data. It notes that genes are not the full story and that the metabolome is the most accessible and dynamically changing molecular phenotype. It describes how investigating metabolomes at large scale can help disentangle the exposome conundrum. Phenome centers are emerging around the world to study over 100,000 patient samples per year, generating several petabytes of data annually. The MetaboLights database serves as an experimental repository for this type of data.
The document discusses the Kyoto Encyclopedia of Genes and Genomes (KEGG), which is an online database that contains information on genomes, enzymatic pathways, and biological chemicals. KEGG aims to computerize current biological knowledge and provide consistent annotations. It maintains six main databases: KEGG Pathway, KEGG Genes, KEGG Genome, KEGG Ligand, KEGG BRITE, and KEGG Cancer. These databases contain information on metabolic pathways, gene catalogs, genome sequences, chemical reactions, functional hierarchies, and cancer pathways respectively. KEGG can be used to detect enzyme clusters, compare gene clusters across genomes, and model and simulate biological systems.
This document discusses alternative funding models for independent scientists conducting rare disease research, including crowdfunding, venture philanthropy, and patronage. It questions how much basic research on model organisms has facilitated drug discovery for rare diseases. It also examines potential hybrid business models and partnerships that could scale up rare disease drug discovery efforts. Finally, it considers whether patronage could compete with venture capital and government grants in funding rare disease research.
Using the Semantic Web to Support Ecoinformaticsebiquity
We describe our on-going work in using the semantic web in support of ecological informatics, and demonstrate a distributed platform for constructing end-to-end use cases. Specifically, we describe ELVIS (the Ecosystem Location Visualization and Information System), a suite of tools for constructing food webs for a given location, and Triple Shop, a SPARQL query interface which allows scientists to semi-automatically construct distributed datasets relevant to the queries they want to ask. ELVIS functionality is exposed as a collection of web services, and all input and output data is expressed in OWL, thereby enabling its integration with Triple Shop and other semantic web resources.
The Kyoto Encyclopedia of Genes and Genomes (KEGG) is a collection of online databases containing information on genomes, enzymatic pathways, and biological chemicals. KEGG aims to computerize current biological knowledge, provide consistent genome annotations, and develop new informatics technologies. It contains six main databases - KEGG Pathway, KEGG Genes, KEGG Genome, KEGG Ligand, KEGG BRITE, and KEGG Cancer - that catalog pathways, genes, genomes, chemical reactions, functional hierarchies, and cancer pathways respectively.
The document is a template for conducting a GAP analysis across multiple business units. It identifies current and goal states for over 25 target items across 14 business functions. The target items generally relate to implementing new processes, systems, or metrics. Each item includes a timeline for achieving the goal state and proposed action items to close the identified GAPs.
This document discusses 7 quality tools used in continuous improvement workshops: affinity diagram, relations diagram, tree diagram, matrix diagram, matrix data analysis, arrow diagram, and process decision program chart. It provides a brief overview of each tool, including what it is used for and typical situations where each tool would be applicable.
Hm Auto Bench Mark Gap Analysis Report 19.09.08guest7b07b10
This document contains a summary of gaps identified during an audit of H.M Auto Industries on 19 September 2008. It lists 88 categories where improvements are needed, such as organizing the raw material storage area, implementing 5S practices in various areas, improving machine maintenance processes, and ensuring proper safety measures throughout the facility. For each category, it identifies the responsible persons and target dates for completing the improvements.
This document outlines the class schedule for a 2013 broadcasting and service design class taught by jylee. The 15-week course covers topics like introducing new user-centered services and interactions in broadcasting environments, service design methodologies, user research methods, idea generation techniques, and prototyping services. The class employs strategies such as affinity mapping, personas, customer journey mapping, and service blueprints to move from defining problems to proposing solutions.
The document provides an overview of 7 management tools: Affinity Diagram, Interrelationship Diagraph, Tree Diagram, Matrix Diagrams, Prioritization Matrix, Process Decision Program Charts (PDPC), and Activity Network Diagrams. It defines each tool, explains how to use it through examples, and illustrates the tools with diagrams. The tools are designed to help structure thinking, simplify complex problems, improve analysis, and facilitate planning and decision making.
Mapping the value of your customers journeyEthology
The game has changed with customer engagement! Go beyond just "journey-mapping" and understand the micro-moments of your customer's entire process of interaction with your brand. There are right and wrong moments of content implementation that could be costing you profit!
Get more insights on the following:
- Customers are in the driver seat with engagement points more often than the brand
- User Experience (UX) can illuminate the customer journey and find more meaningful ways to connect with them
- True strategy and planning are a process that must be ongoing versus just a "start-point"
SPEAKER:
Anthony Quiroz, UX Design Strategist at Ethology
Structuring for success - Developing a dynamic structure for your marketing t...B2B Marketing
With marketing evolving rapidly in response to adoption of emerging digital communication techniques and changing buyer behaviour, it's imperative that the skill set of the marketing function evolves too, to reflect this and to enable the brand to compete effectively in the digital age.
Furthermore, marketing must be able to concisely communicate and report on the value of what they are delivering for the organisation, to all departments and particularly to the board. Fresh from delivering Deloitte's Olympics sponsorship, brand and marketing director Annabel Pritchard will focus on how to build a marketing function that's fit for purpose and structured around delivering clear and measurable business benefits. This session will cover:
•Structuring the team - ensuring a dynamic mix of specialisms across the marketing function
•Managing and nurturing the marketing team - encouraging learning and skills development
•Raising the profile of marketing - reporting value to the Board and championing the value of marketing across the business.
The document outlines the evolution of marketing departments from simple sales departments to modern process- and outcome-based companies, tracing the growth of dedicated marketing teams and functions over five stages: from sales-only to integrated sales and marketing teams to separate departments to modern cross-functional organizations focused on processes and outcomes.
The document summarizes several management tools including affinity diagrams, interrelationship diagrams, tree diagrams, matrix diagrams, and prioritization matrices. It provides definitions and examples of how each tool can be used to structure brainstorming, analyze relationships between factors, break processes down into detailed levels, compare relationships between groups, and prioritize items according to weighted criteria. The tools are designed to help simplify complex problems, structure thinking, and improve decision making.
How to design a modern Marketing and Communications department in an agile ma...Paul Cowan
Marketing departments still remain in an old, hierarchical structure with a massive reliance on agencies and vendors to do much of the brand positioning and communications work. This model is inefficient, outdated and removes the IP from the ownership of the company. This document reveal the 3 key issues that are forcing change on how marketing organizations structure and deploy, with a recommended structure and people required in the modern marketing world.
Modern marketing organizational structure @kaykas - jascha kaykas-wolffJascha Kaykas-Wolff
Organizational design and restructuring is not new. But, with the requirement to create data-driven marketing organizations and support marketers who show bottom line results more emphasis is being placed on marketing leaders to structure their teams and business in a way that is agile and impactful.
Reflecting on this, and doing some additional research of my own, I was struck by the lack of published material describing how one might go about building a marketing organization that addresses business challenges happening right now and most importantly that can drive results right now.
Over the past several years as I’ve been fortunate to lead marketing organizations for enterprise and mid-market businesses. During this time I’ve developed an organizational playbook that can scale to virtually any size of business, is highly adaptable, and has a proven track record for success.
Enclosed is the core framework for what I believe is an ideal composition for the modern marketing organization. I’m looking forward to your feedback. - Jascha
The 10 responsibilities of marketing departmentsSales Layer
In many companies, marketing departments turned into a kind of catch-all... But what are their real responsibilities?
In this post you’ll find 10 tasks that are the responsibility of the marketing department. All of them have a crucial importance in ensuring the survival of your company.
Biodiversity informatics and the agricultural data landscapeCyndy Parr
Introductory talk of a symposium on Agrobiodiversity informatics at the 2016 annual meeting of the Biodiversity Information Standards. Begins with an overview of the symposium and its speakers, and then launches into my talk.
A state-of-the-art biorepository: Challenges and opportunitiesILRI
Presentation by Absolomon Kihara and Steve Kemp at the third Medical and Veterinary Virus Research Symposium (MVVR-3), Nairobi, Kenya, 17 October 2014.
Azizi biorepository: Challenges and opportunitiesILRI
Presentation by Absolomon Kihara and Steve Kemp at an ILRI seminar on managing biological samples held at the ILRI Nairobi campus on 10 September 2013.
Presentation by Simon Mayo at the KikForum
Abstract:
As part of the CATE project we are developing keys in Lucid 3 to the genera of Araceae, and to the genus Anthurium (ca. 800spp.), Arum and Philodendron. The key to Arum is already online. These keys will be incorporated into a web-based taxonomic revision of the Araceae family as the plant model group for the project. Anthurium presents a particular challenge as it is a very large and difficult genus, within which it is currently nearly impossible for non-specialists to determine plants to species. We hope the key will go some way to solving this problem.
Large Scale computing with medical metabolic phenotyping dataChristoph Steinbeck
This document discusses large scale computing with medical metabolic phenotyping data. It notes that genes are not the full story and that the metabolome is the most accessible and dynamically changing molecular phenotype. It describes how investigating metabolomes at large scale can help disentangle the exposome conundrum. Phenome centers are emerging around the world to study over 100,000 patient samples per year, generating several petabytes of data annually. The MetaboLights database serves as an experimental repository for this type of data.
The document discusses the Kyoto Encyclopedia of Genes and Genomes (KEGG), which is an online database that contains information on genomes, enzymatic pathways, and biological chemicals. KEGG aims to computerize current biological knowledge and provide consistent annotations. It maintains six main databases: KEGG Pathway, KEGG Genes, KEGG Genome, KEGG Ligand, KEGG BRITE, and KEGG Cancer. These databases contain information on metabolic pathways, gene catalogs, genome sequences, chemical reactions, functional hierarchies, and cancer pathways respectively. KEGG can be used to detect enzyme clusters, compare gene clusters across genomes, and model and simulate biological systems.
This document discusses alternative funding models for independent scientists conducting rare disease research, including crowdfunding, venture philanthropy, and patronage. It questions how much basic research on model organisms has facilitated drug discovery for rare diseases. It also examines potential hybrid business models and partnerships that could scale up rare disease drug discovery efforts. Finally, it considers whether patronage could compete with venture capital and government grants in funding rare disease research.
Using the Semantic Web to Support Ecoinformaticsebiquity
We describe our on-going work in using the semantic web in support of ecological informatics, and demonstrate a distributed platform for constructing end-to-end use cases. Specifically, we describe ELVIS (the Ecosystem Location Visualization and Information System), a suite of tools for constructing food webs for a given location, and Triple Shop, a SPARQL query interface which allows scientists to semi-automatically construct distributed datasets relevant to the queries they want to ask. ELVIS functionality is exposed as a collection of web services, and all input and output data is expressed in OWL, thereby enabling its integration with Triple Shop and other semantic web resources.
The Kyoto Encyclopedia of Genes and Genomes (KEGG) is a collection of online databases containing information on genomes, enzymatic pathways, and biological chemicals. KEGG aims to computerize current biological knowledge, provide consistent genome annotations, and develop new informatics technologies. It contains six main databases - KEGG Pathway, KEGG Genes, KEGG Genome, KEGG Ligand, KEGG BRITE, and KEGG Cancer - that catalog pathways, genes, genomes, chemical reactions, functional hierarchies, and cancer pathways respectively.
The document is a template for conducting a GAP analysis across multiple business units. It identifies current and goal states for over 25 target items across 14 business functions. The target items generally relate to implementing new processes, systems, or metrics. Each item includes a timeline for achieving the goal state and proposed action items to close the identified GAPs.
This document discusses 7 quality tools used in continuous improvement workshops: affinity diagram, relations diagram, tree diagram, matrix diagram, matrix data analysis, arrow diagram, and process decision program chart. It provides a brief overview of each tool, including what it is used for and typical situations where each tool would be applicable.
Hm Auto Bench Mark Gap Analysis Report 19.09.08guest7b07b10
This document contains a summary of gaps identified during an audit of H.M Auto Industries on 19 September 2008. It lists 88 categories where improvements are needed, such as organizing the raw material storage area, implementing 5S practices in various areas, improving machine maintenance processes, and ensuring proper safety measures throughout the facility. For each category, it identifies the responsible persons and target dates for completing the improvements.
This document outlines the class schedule for a 2013 broadcasting and service design class taught by jylee. The 15-week course covers topics like introducing new user-centered services and interactions in broadcasting environments, service design methodologies, user research methods, idea generation techniques, and prototyping services. The class employs strategies such as affinity mapping, personas, customer journey mapping, and service blueprints to move from defining problems to proposing solutions.
The document provides an overview of 7 management tools: Affinity Diagram, Interrelationship Diagraph, Tree Diagram, Matrix Diagrams, Prioritization Matrix, Process Decision Program Charts (PDPC), and Activity Network Diagrams. It defines each tool, explains how to use it through examples, and illustrates the tools with diagrams. The tools are designed to help structure thinking, simplify complex problems, improve analysis, and facilitate planning and decision making.
Mapping the value of your customers journeyEthology
The game has changed with customer engagement! Go beyond just "journey-mapping" and understand the micro-moments of your customer's entire process of interaction with your brand. There are right and wrong moments of content implementation that could be costing you profit!
Get more insights on the following:
- Customers are in the driver seat with engagement points more often than the brand
- User Experience (UX) can illuminate the customer journey and find more meaningful ways to connect with them
- True strategy and planning are a process that must be ongoing versus just a "start-point"
SPEAKER:
Anthony Quiroz, UX Design Strategist at Ethology
Structuring for success - Developing a dynamic structure for your marketing t...B2B Marketing
With marketing evolving rapidly in response to adoption of emerging digital communication techniques and changing buyer behaviour, it's imperative that the skill set of the marketing function evolves too, to reflect this and to enable the brand to compete effectively in the digital age.
Furthermore, marketing must be able to concisely communicate and report on the value of what they are delivering for the organisation, to all departments and particularly to the board. Fresh from delivering Deloitte's Olympics sponsorship, brand and marketing director Annabel Pritchard will focus on how to build a marketing function that's fit for purpose and structured around delivering clear and measurable business benefits. This session will cover:
•Structuring the team - ensuring a dynamic mix of specialisms across the marketing function
•Managing and nurturing the marketing team - encouraging learning and skills development
•Raising the profile of marketing - reporting value to the Board and championing the value of marketing across the business.
The document outlines the evolution of marketing departments from simple sales departments to modern process- and outcome-based companies, tracing the growth of dedicated marketing teams and functions over five stages: from sales-only to integrated sales and marketing teams to separate departments to modern cross-functional organizations focused on processes and outcomes.
The document summarizes several management tools including affinity diagrams, interrelationship diagrams, tree diagrams, matrix diagrams, and prioritization matrices. It provides definitions and examples of how each tool can be used to structure brainstorming, analyze relationships between factors, break processes down into detailed levels, compare relationships between groups, and prioritize items according to weighted criteria. The tools are designed to help simplify complex problems, structure thinking, and improve decision making.
How to design a modern Marketing and Communications department in an agile ma...Paul Cowan
Marketing departments still remain in an old, hierarchical structure with a massive reliance on agencies and vendors to do much of the brand positioning and communications work. This model is inefficient, outdated and removes the IP from the ownership of the company. This document reveal the 3 key issues that are forcing change on how marketing organizations structure and deploy, with a recommended structure and people required in the modern marketing world.
Modern marketing organizational structure @kaykas - jascha kaykas-wolffJascha Kaykas-Wolff
Organizational design and restructuring is not new. But, with the requirement to create data-driven marketing organizations and support marketers who show bottom line results more emphasis is being placed on marketing leaders to structure their teams and business in a way that is agile and impactful.
Reflecting on this, and doing some additional research of my own, I was struck by the lack of published material describing how one might go about building a marketing organization that addresses business challenges happening right now and most importantly that can drive results right now.
Over the past several years as I’ve been fortunate to lead marketing organizations for enterprise and mid-market businesses. During this time I’ve developed an organizational playbook that can scale to virtually any size of business, is highly adaptable, and has a proven track record for success.
Enclosed is the core framework for what I believe is an ideal composition for the modern marketing organization. I’m looking forward to your feedback. - Jascha
The 10 responsibilities of marketing departmentsSales Layer
In many companies, marketing departments turned into a kind of catch-all... But what are their real responsibilities?
In this post you’ll find 10 tasks that are the responsibility of the marketing department. All of them have a crucial importance in ensuring the survival of your company.
Here are some key responsibilities and skills for a Product Manager vs Product Marketing Manager role:
Product Manager:
- Responsibilities: Define product requirements, ensure product gets developed on time and on budget, own product roadmap/strategy.
- Skills: Strong technical skills, able to understand customer needs and translate to technical requirements, able to manage cross-functional teams.
Product Marketing Manager:
- Responsibilities: Develop product marketing strategy and messaging, generate demand through campaigns, manage product launch.
- Skills: Strong marketing, communications and presentation skills, able to understand customer needs from a non-technical perspective, experience with demand generation and analytics.
The main differences are that the Product Manager role requires more
HubSpot partnered with innovative executives from Forrester Research, Mindjet, Rue La La, Zendesk, Atlassian, and GitHub to bring you this look into modern-day marketing org structure. As inbound and digital change the way we market, we need to stay ahead in the way we organize our teams. In this report, each executive details their org chart and looks ahead to the future. You can also download each job description found in the report for your company to use!
This document discusses gap analysis, a tool used to assess crop genetic and geographical diversity. It allows identifying areas where species collections are lacking and prioritizing species and locations for future collection efforts. The process involves reviewing taxonomy, gathering data on species distributions and environments, and identifying gaps in ex situ conservation coverage. Taxa are then prioritized as high, medium, or low priority for conservation. Results are publicly available and include recommendations on priority taxa to collect, maps of collection locations, and methodology details.
The document discusses the importance of data related to plant genetic resources for food and agriculture (PGRFA) accessions stored in genebanks. It covers different types of data like characterization data, evaluation data, environmental data, and genetic data. It emphasizes that without proper data, accessions in genebanks are worthless. The document also discusses standards and schemas for managing characterization and evaluation data, like those used by the USDA National Plant Germplasm System and GRIN-Global portal. The overall goal of managing this data should be facilitating the effective utilization of PGRFA accessions.
This document summarizes a study that identified global priorities for collecting and conserving crop wild relatives. The study analyzed 1079 crop wild relative taxa for 81 globally important crops. Researchers gathered occurrence data from 420 sources and modeled species distributions to measure sampling, geographic, and ecological representativeness. This identified collecting "hotspots" and prioritized taxa for collection. The results support ex situ conservation of crop wild relatives by targeting areas and species that will fill gaps in collections.
Presentation made by Andy Jarvis in the Latin American Congress of Chemistry on 30th September 2010, in the symposium on Biodiversity and Ecosystems: the role of the chemical sciences.
This document discusses the rise of big data in modern microbiology due to advances in DNA sequencing technologies. It notes that while sequencing is now much cheaper and faster, analyzing the large volumes of sequencing data presents new computational challenges. Methods like digital normalization are helping to scale down datasets for assembly. While sequencing is revealing vast unknown diversity in communities like soil, connecting patterns in the data to biological functions and mechanisms remains difficult. Collaboration and data sharing will be important to advance the field.
Andy J Value Of A Coordinate Montpellier Nov 2009CIAT
Presentation at TDWG 2009 in montpellier on the value of geographic coordinates for exploring agricultural biodiversity patterns, and influencing conservation policy.
Presentation made by Andy Jarvis from the Decision and Policy Analysis Program of the International Centre for Tropical Agriculture (CIAT). Delivered at the TDWG conference 2009 in Montpellier, France in November.
Marco Brandizi and Keywan Hassani-Pak, Rothamsted Research, Invited Presentation at SWAT4HCLS 2022.
FAIR data principles are being a driving force in life sciences and other scientific domains, helping researchers to share their data and free all of their potential to integrate information and do novel discoveries. Knowledge graphs are an ever more popular paradigm to model data according to such principles, and technologies such as graph databases are emerging as complementary to approaches like linked data. All of this includes the agronomy, farming and food domains. How advanced the adoption of sound data management policies is in these life domains? How does that compare to other life sciences? In this presentation, we will talk about our practical experience, focusing on KnetMiner, a gene and molecular biology discovering platform, which is based on building and publishing knowledge graphs according to the FAIR principles, as well as using a mix of linked data standards for life sciences and recent graph database and API technologies. We will welcome questions and discussions from the audience about similar experience.
This document discusses the need for a soil-specific reference database to connect soil metagenomic sequencing data at different levels and enable broader understanding of soil health and productivity. It outlines challenges in soil metagenomics like incredible microbial diversity and lack of reference genomes. Lessons are drawn from the Human Microbiome Project reference genome effort. A targeted sequencing approach could benefit soil studies by providing frameworks for sequencing and identification. Challenges include defining soil organisms and important metadata. Initial efforts like RefSoil and NCBI Reference Genomes from soil are noted but require further curation. Contributions to developing such a database are welcomed.
Scientific data is used to assess environmental risk and ensure biodiversity conservation in several ways:
1) Qualitative and quantitative methods like indices are used to measure biodiversity levels and threats.
2) Environmental impact assessments require developers to identify potential effects and propose safeguards to reduce impacts.
3) The precautionary principle places the burden of proof on actions that could harm the environment when risks are uncertain.
4) Risk analysis uses hypothesis testing and comparisons to evaluate probabilities of species extinction.
Trait Mining, prediction of agricultural traits in plant genetic resources with ecological parameters. Focused Identification of Germplasm Strategy (FIGS). For the Vavilov seminars at the IPK Gatersleben 13th June 2007. Dag Endresen, Michael Mackay, Kenneth Street.
This document discusses the challenges of analyzing large datasets from metagenomic shotgun sequencing experiments. It notes that while sequencing costs have decreased significantly, the computational analysis of the massive amounts of data generated still poses major challenges. It introduces the concept of "digital normalization" as an approach to reduce dataset sizes while retaining most of the biological information by removing redundant reads. The document advocates for making analysis tools and datasets openly accessible to help advance understanding of microbial communities from metagenomics studies.
This document discusses challenges and opportunities for discovering and documenting biodiversity in the current information age. It argues that current taxonomic processes are too slow and that new approaches are needed to integrate distributed data sources and leverage community contributions. Specifically, it proposes:
1) Publishing new biodiversity data prior to formal documentation to accelerate discovery.
2) Developing automated workflows and online workspaces to integrate phylogenetic, distribution, and trait data.
3) Enabling community participation through open data sharing and collaborative annotation platforms.
This document discusses challenges and opportunities for discovering and documenting biodiversity in the current information age. It argues that current taxonomic processes are too slow and that new approaches are needed to integrate distributed data sources and leverage community sourcing. Specifically, it advocates for:
1) Publishing new biodiversity data prior to formal documentation to accelerate discovery.
2) Developing automated workflows and online workspaces to integrate phylogenetic, distribution, and trait data.
3) Enabling community participation in annotating and improving global biodiversity models and maps.
4) Changing incentives to value data sharing over individual "kudos" and prioritize the collective good of the scientific community.
This document summarizes a gap analysis conducted on the genetic diversity of potato crops. Gap analysis is a tool used to assess levels of crop genetic and geographic diversity currently held in ex situ conservation systems. It identifies taxa that are high priorities for further collection to fill gaps, as well as their geographic locations. The analysis found that two varieties within the Rugosi and Acutifolii sections of potato - P. carteri and P. acutifolius var. latifolius, respectively - were high priority for further collection. It also provides maps indicating priority areas to collect these taxa. The methodology and results of this and other crop gap analyses are publicly available online.
New concepts in maintenance of plant breeding promises and prospectsZuby Gohar Ansari
1. The document discusses new concepts in plant breeding that promise to improve crops, including exploiting genes from wild plants and breaking complex traits into components to select for improved crops.
2. Recent advances in breeding technology such as wide hybridization between crops and wild relatives, molecular marker-assisted selection, and selecting for quantitative trait components are allowing plant breeders to make faster progress in improving yields and stress tolerance.
3. While genetic engineering holds promise, conventional plant breeding continues to advance and ensure contributions to agriculture through increasingly sophisticated methods.
Building bioinformatics resources for the global communityExternalEvents
1. The document evaluates different methods for inferring relationships between Salmonella samples based on whole genome sequencing data from large databases. It compares k-mer based methods and site-based methods using 18,997 Salmonella isolates from public databases.
2. Site-based methods like NUCmer and MLST produced more accurate results, but require more computing resources when dealing with large databases. K-mer based methods are faster but more sensitive to assembly and contamination issues.
3. While k-mer methods may be useful for initial filtering, site-based methods are superior for accuracy, though challenges remain in applying them to databases containing tens of thousands of samples. Quality control and computing resources are important considerations.
How to transform genomic big data into valuable clinical informationJoaquin Dopazo
This document discusses how to transform genomic big data into valuable clinical information. It begins by defining genomic big data and explaining how individual genome data contains more information than the original experiment. Next, it discusses lessons learned from genome-wide association studies, including that many loci contribute to traits and there is evidence of pleiotropy. However, individual genes cannot fully explain trait heritability. The document then discusses challenges in detecting disease-related variants from exome/genome sequencing data due to the large number of variants and presence of apparently deleterious variants in healthy individuals. It suggests taking a systems approach considering interactions and multigenicity to better understand variation and disease mechanisms.
Similar to Andy J Gap analysis and crop wild relatives bellagio sept 2010 (20)
Fortalecimiento de capacidades para la producción, traducción, diseminación y uso efectivo de datos y perspectivas climáticas en el sector agropecuario en la región SICA.
Carlos Navarro-Racines
Evento de socialización de los logros alcanzados por CCAFS en Centroamérica en el marco de la gira del Grupo Técnico de Cambio Climático y Gestión Integral del Riesgo (GTCCGIR) del CAC.
Guatemala, diciembre 1, 2021
1) El documento describe los Servicios Integrados Participativos de Clima para la Agricultura (PICSA), un enfoque para empoderar a los agricultores con información climática y herramientas de toma de decisiones.
2) PICSA se ha implementado en varios países de América Latina con el objetivo de mejorar la resiliencia climática y la seguridad alimentaria.
3) El documento propone fortalecer la cadena de servicios climáticos en Guatemala mediante la capacitación de técnicos, la implementación de PIC
El documento discute los desafíos y oportunidades del cambio climático para la agricultura en Centroamérica. La variabilidad climática afecta entre un 32-39% de la productividad de los cultivos y los sistemas no son resilientes. Se requiere adaptación a diferentes escalas de tiempo, desde días hasta décadas. Existe una brecha entre la información climática y su uso por los agricultores. Los servicios climáticos buscan cerrar esta brecha mediante mejoras en predicciones, empoderamiento e instituciones. Enfoques como las
Servicios climáticos para la agricultura: Incorporando información agroclimática local en la toma de decisiones.
Feria Internacional del Medio Ambiente (FIMA)
Servicios climáticos para la agricultura: Incorporando información agroclimática local en la toma de decisiones
Webinar: Recursos De Información Para El Sector Agrícola En La Región De America Latina Y El Caribe.
Plataforma de Acción Climática en Agricultura de Latinoamérica y el Caribe (PLACA)
Presentación del Módulo 2 "El cambio climático, retos y desafíos para el desarrollo sostenible" del diplomado “El cambio climático y el sector agropecuario: desafíos y oportunidades para un desarrollo resiliente, con bajas emisiones y adaptado al clima en Centroamérica y República Dominicana.
Instituto Centroamericano de Administración Pública (ICAP)
En el marco del LXIV Foro del Clima de América Central y
el XLII Foro de Aplicaciones de los Pronósticos Climáticos
a la Seguridad Alimentaria y Nutricional
Academia Nacional de Servicios Climáticos - Guatemala
Diplomado en Ciencias del Clima y Servicios Climáticos del Sistema Guatemalteco de Ciencias del Cambio Climatico (SGCCC)
https://sgccc.org.gt/el-sgccc-es-el-anfitrion-del-diplomado-en-ciencias-del-clima-y-servicios-climaticos/
Navarro, C. Modelación climática; Cambio climático y agricultura
Clase para Curso de climatología de la Universidad de Ciencias Aplicadas y Ambientales (UDCA)
Abril 2021
Este documento describe los servicios climáticos y su importancia para los agricultores. Explica que los agricultores necesitan información climática para tomar decisiones, pero a menudo no pueden acceder a ella o comprenderla. Los servicios climáticos buscan cerrar esta brecha mediante la producción, traducción y transferencia de conocimientos climáticos para apoyar la toma de decisiones. También describe las Mesas Técnicas Agroclimáticas, que reúnen a actores locales para discutir las mejores prácticas de adaptación y
Webinario: Modelación de cultivos para generar servicios
agroclimáticos (AquaCrop v.6)
LXI Foro del Clima de América Central
Jeferson Rodriguez Espinoza
Alejandra Esquivel
Carlos Navarro-Racines
J. Ramírez , D. Martínez, A. Martínez, J. Martínez, D. Giraldo, A. Muller, C. Bouroncle
Diplomado el enfoque territorios sostenibles adaptados al clima (TeSAC) en el corredor seco del oriente de Guatemala
Módulo 2 – Bloque 2 – Sesión 3
Carlos Navarro-Racines
E. Tünnermann, J. Ramírez, A. Martínez, J. Martínez
Diplomado “Inventario de Emisiones de Gases de Efecto Invernadero”, Universidad Nacional Agraria (UNA)
Módulo I Introducción. Procesos nacionales (políticas y convenios nacionales e internacionales)
Sesión 1 Introducción a la problemática del cambio climático global y observación de cambios
Este documento describe el uso de servicios climáticos para mejorar la agricultura en América Latina. Presenta las Mesas Técnicas Agroclimáticas y los Servicios Integrados Participativos de Clima para la Agricultura como enfoques para proporcionar información climática relevante a los agricultores de manera que puedan tomar mejores decisiones. También describe cómo estos enfoques han ayudado a los agricultores a adaptarse al cambio climático y reducir las pérdidas debido a la variabilidad climática.
Importancia de los pronósticos aplicados al sector durante la crisis actual del COVID-19
XLI Foro de Aplicación de los Pronósticos Climáticos a la Seguridad Alimentaria y Nutricional: Perspectivas para el período Agosto - Octubre 2020 - 22 de julio del 2020
Presentación sobre las Mesas Técnicas Agroclimáticas en Centro América en el contexto de COVID-19, en el marco del webinar "Desafíos y oportunidades para alcanzar equidad de género en los servicios climáticos"
Training on Participatory Integrated Climate Services for Agriculture (PICSA) and Local Technical Agroclimatic Comittees (MTA / LTAC) to the DeRISK project team.
February 11 -19 2020, CIAT Hanoi, Vietnam
Este documento describe cómo las Mesas Técnicas Agroclimáticas (MTA) apoyan la toma de decisiones de los agricultores en el contexto de la variabilidad climática y la pandemia de COVID-19 a través de boletines agroclimáticos, recomendaciones para prácticas agrícolas apropiadas al clima y extensión remota. El objetivo es reducir los riesgos climáticos y socioeconómicos que enfrentan los agricultores debido a la pandemia a través del monitoreo, difusión de
More from Decision and Policy Analysis Program (20)
2. Why Gap Analysis? Tool to assess crop and crop wild relative genetic and geographical diversity Allows detecting incomplete species collections as well as defining which species should be collected and where these collections should be focused Assesses the current extent at which the ex situ conservation system is correctly holding the genetic diversity of a particular genepool
3. To know what you don’t have, you first need to know what you do have….and that’s where things already get complex
21. Wild Vigna collecting priorities Spatial analysis on current conserved materials *Gaps* in current collections Definition and prioritisation of collecting areas 8 100x100km cells to complete collections of 23 wild Vigna priority species
22.
23. Even better: resistance distance McRae, B.H. 2006. Isolation by resistance. Evolution 6(8), 1551-1561.
32. Conclusions and open-ended issues Gap analysis can focus priorities for collecting, and cost/benefit lies in collecting multiple genepools simultaneously But, analysis as good as input data If you can’t see the data, is the collection valid? Multiple methods available Key question: what is a “complete” collection?