This document summarizes a talk on open science given by Jonathan Eisen. Some key points:
1. Eisen recounted his early skepticism of open access but eventual conversion after experiences like publishing an open access paper that received more attention.
2. He discussed experiments with openly releasing genomic data that helped convince him of the benefits of openness in science.
3. Eisen argued that limiting access to scientific literature and data hinders scientific progress, and outlined several ways scientists can promote openness.
The document discusses open science and open access. It provides examples of open science like open access publishing, open notebooks, prepublication data release, and open source software. It discusses three aspects of open science: cost, restrictions, and timing. It discusses the costs of publishing, creative commons licenses, and examples of organizations that promote open access like the Public Library of Science (PLoS) and how they circulated an open letter to encourage open access. Overall, the document discusses the history and concepts of open science and open access.
Open Knowledge and University of Cambridge European Bioinformatics InstituteTheContentMine
This document discusses open data and open science. It highlights Jean-Claude Bradley as a pioneer of open notebook science and open data who believed closed data means people die. It describes tools like ContentMine that can automatically extract data like chemical reactions, phylogenetic trees and clinical trial results from papers. Visitors can extract specific types of data while repositories can solve problems communally with continuous publication and validation.
The document discusses the opportunities that open science provides and the challenges of implementing open science practices. It argues that open science allows data and research to have a longer lifespan by enabling others to build upon it. While making data and methods openly available requires extra effort, databases and tools are helping to make open science practices more practical. The document urges researchers to look beyond just preventing bad practices and to focus on the potential benefits of open science, such as maximizing the usefulness of research and stimulating new discoveries.
This document summarizes the history and evolution of open access scientific publishing, focusing on the role of the Public Library of Science (PLoS). It discusses how PLoS pioneered open access publishing through petitions and journals in 2001. It then covers how PLoS helped establish PubMed Central and advocated for policies like the NIH public access policy. The document outlines PLoS's current experiments with metrics, commenting tools, and other innovations to improve access and reuse of research.
GMOD in the Cloud provides preinstalled GMOD tools like Tripal, Chado, GBrowse, and JBrowse on cloud.gmod.org. These tools allow users to visualize, annotate, and manage biological data in the cloud. Potential use cases include community annotation events where users can load data, configure tools, annotate, and then export annotations without installing software locally. Using the cloud avoids installation issues and saves money while providing access to sample genomic datasets.
The document discusses how integrative studies can provide insights through combining candidate genomic regions, mitochondrial proteomic data, and cancer expression compendiums to discover genes involved in diseases like Leigh Syndrome and cancers. It also highlights several other studies that have integrated data like DNA sequences, copy numbers, methylation, expression profiles, and pathways to characterize disease subtypes and improve risk stratification for conditions such as glioblastoma multiforme and medulloblastoma. The document presents an example of a translational research study that integrated multiple genomic data types and computational tools in 12 steps to analyze alterations in gene expression and identify potential transcription factor binding sites.
P Rocca-Serra - The open source ISA metadata tracking framework: from data cu...Jan Aerts
Presentation at BOSC2012 by P Rocca-Serra - The open source ISA metadata tracking framework: from data curation and management at the source, to the linked data universe
The document discusses open science and open access. It provides examples of open science like open access publishing, open notebooks, prepublication data release, and open source software. It discusses three aspects of open science: cost, restrictions, and timing. It discusses the costs of publishing, creative commons licenses, and examples of organizations that promote open access like the Public Library of Science (PLoS) and how they circulated an open letter to encourage open access. Overall, the document discusses the history and concepts of open science and open access.
Open Knowledge and University of Cambridge European Bioinformatics InstituteTheContentMine
This document discusses open data and open science. It highlights Jean-Claude Bradley as a pioneer of open notebook science and open data who believed closed data means people die. It describes tools like ContentMine that can automatically extract data like chemical reactions, phylogenetic trees and clinical trial results from papers. Visitors can extract specific types of data while repositories can solve problems communally with continuous publication and validation.
The document discusses the opportunities that open science provides and the challenges of implementing open science practices. It argues that open science allows data and research to have a longer lifespan by enabling others to build upon it. While making data and methods openly available requires extra effort, databases and tools are helping to make open science practices more practical. The document urges researchers to look beyond just preventing bad practices and to focus on the potential benefits of open science, such as maximizing the usefulness of research and stimulating new discoveries.
This document summarizes the history and evolution of open access scientific publishing, focusing on the role of the Public Library of Science (PLoS). It discusses how PLoS pioneered open access publishing through petitions and journals in 2001. It then covers how PLoS helped establish PubMed Central and advocated for policies like the NIH public access policy. The document outlines PLoS's current experiments with metrics, commenting tools, and other innovations to improve access and reuse of research.
GMOD in the Cloud provides preinstalled GMOD tools like Tripal, Chado, GBrowse, and JBrowse on cloud.gmod.org. These tools allow users to visualize, annotate, and manage biological data in the cloud. Potential use cases include community annotation events where users can load data, configure tools, annotate, and then export annotations without installing software locally. Using the cloud avoids installation issues and saves money while providing access to sample genomic datasets.
The document discusses how integrative studies can provide insights through combining candidate genomic regions, mitochondrial proteomic data, and cancer expression compendiums to discover genes involved in diseases like Leigh Syndrome and cancers. It also highlights several other studies that have integrated data like DNA sequences, copy numbers, methylation, expression profiles, and pathways to characterize disease subtypes and improve risk stratification for conditions such as glioblastoma multiforme and medulloblastoma. The document presents an example of a translational research study that integrated multiple genomic data types and computational tools in 12 steps to analyze alterations in gene expression and identify potential transcription factor binding sites.
P Rocca-Serra - The open source ISA metadata tracking framework: from data cu...Jan Aerts
Presentation at BOSC2012 by P Rocca-Serra - The open source ISA metadata tracking framework: from data curation and management at the source, to the linked data universe
Opening up Scientific and Scholarly CommunicationJonathan Eisen
The document discusses the history and goals of the Public Library of Science (PLoS), an organization founded in 2000 to promote open access scientific publishing. PLoS circulated an open letter calling for freely accessible scientific literature and launched their own open access journals, PLoS Biology and PLoS Medicine, after not enough publishers supported open access. The document also describes the author's personal experience with lack of access to scientific papers delaying treatment for his stillborn son, which reinforced his views that limiting access is unethical and counterproductive to advancing scientific knowledge.
PLOS (Public Library of Science) is a nonprofit open-access publisher founded in 2001 with a mission to accelerate scientific progress. PLOS makes research articles immediately and freely available worldwide under open-access licenses. It publishes several peer-reviewed journals covering various scientific fields like biology, medicine, and genetics. PLOS advocates for openness in science through open data sharing, transparent peer review processes, and making research outputs openly accessible for all.
Opening up to Diversity talk by @phylogenomics at #UCDPHSAJonathan Eisen
This document summarizes the key points of an article on the diversity and composition of bacteria in indoor environments. It finds that the bacterial communities found indoors are less diverse than outdoors, and that mechanically ventilated rooms contain less diverse communities than window ventilated rooms. Certain building attributes like ventilation source, airflow rates, humidity and temperature are correlated with the diversity and types of bacteria present. Rooms with lower airflow and humidity have higher abundances of potential human pathogens. The study suggests that building design and operation can manage the indoor microbiome and species that may colonize the human microbiome.
Presentation given at Open Science question and answer session hosted by the Institute for Quantitative Social Science (IQSS), and the Office for Scholarly Communication (OSC) at Harvard University, on July 16th 2014.
Bringing the Social Media Revolution to Thoracic SurgeryMayo Clinic
The document discusses bringing social media to thoracic surgery and the AATS 2013 annual meeting. It provides details on the scientific program, guest lectures, and social events at the meeting. It also describes the objectives and activities of the Mayo Clinic Center for Social Media, including their work to promote the use of social media in healthcare. Finally, it discusses Lee Aase's background and objectives for the webinar on applying social media in clinical practice, education, and research.
Open Data and Open Science presented in Rio for Open Science 2014-08-22. I argue that Open Notebook Science is the way forward and will lead to great benefits
The document discusses the potential for open science and data to disrupt traditional academic institutions by deinstitutionalizing rewards and metrics for scientific research. It argues that fully embracing open practices like data sharing, collaboration and publishing in open access venues is necessary for a more transparent and reproducible scientific process, but that many academic institutions have yet to adapt their reward systems to incentivize these activities. The talk outlines steps the scientific community can take to further this transition, such as developing community resources and standards, educating peers, and recognizing the different roles that institutions need to play to support open scholarship.
The document discusses several researchers' views on open access publishing. It summarizes that the researchers believe research funded by public money should be accessible to the public, open access removes barriers to research, and that it builds research capacity globally. However, some note that open access publishing costs can be high.
- Research results should be accessible to the public. The outputs of research funded by public money should serve the general public.
- Open access removes barriers to accessing research outcomes and promotes sharing of scientific knowledge. It also helps build research capacity in developing countries by providing access to journals.
- Open access publishing can have benefits like higher citation rates for articles and allowing broader access to research. However, page charges to publish open access can be expensive.
This document summarizes a digital natives seminar about open access publishing and predatory journals. It discusses rising journal prices, copyright issues for faculty publishing work, different types of open access like gold and green open access. It describes benefits and issues with open access like identifying predatory journals. It provides resources for evaluating journals and understanding publisher policies on self-archiving. It introduces the institutional repository Constellation that Benedictine University uses to provide open access to scholarly works.
This document summarizes a digital natives seminar about open access publishing and predatory journals. It discusses rising journal prices, copyright issues for faculty publishing work, different types of open access like gold and green open access. It describes benefits and issues with open access like identifying predatory journals. It provides resources for evaluating journals and understanding publisher policies on self-archiving. It introduces the institutional repository Constellation that Benedictine University uses to provide open access to scholarly works.
This document summarizes a digital natives seminar about open access publishing and predatory journals. It discusses rising journal prices, copyright issues for faculty publishing work, different types of open access like gold and green open access. It describes benefits and issues with open access like identifying predatory journals. It provides resources for evaluating journals and understanding publisher policies on self-archiving. It introduces the institutional repository Constellation that Benedictine University uses to provide open access to scholarly works.
Scholarly communication: Not just for scholars anymoreJoseph Kraus
This document discusses scholarly communication and open access. It notes that while various organizations push for more open access to research, there are still misunderstandings about open access among scientists, researchers, publishers and librarians. Specifically, some misunderstand behaviors include thinking open access is not needed or that the general public would not understand research articles. The document also discusses how the culture among scientists values traditional peer-reviewed journals and gatekeepers, and is slow to change. It suggests librarians can help address these issues by continuing to observe scientist behaviors and demonstrating the benefits of open access, such as increased citations.
Tina Baich, IUPUI University Library, USA Diminishing the perceived need f...CTLes
This document discusses diminishing unauthorized or "black" open access sharing. It begins with an overview of open access models and levels of black open access from oblivious offenders to hijackers. It then discusses discovery tools like OAB and Unpaywall and a library action plan focusing on improved discovery and delivery integration, educating users, and collection strategies emphasizing open access. The goal is to steer users towards legal options while understanding motivations for unauthorized sharing and how libraries can help meet user needs.
Rethinking the Functions of a Journal - some case studies from PLoS by Mark P...dduin
The document discusses re-engineering scientific journals to better serve their functions of registration, certification, dissemination and preservation. It describes PLoS's efforts to make scientific literature openly accessible online through journals like PLoS Biology and PLoS Medicine. PLoS is working to improve the organization of content by topic and impact, speed up authoring and certification through approaches like PLoS Currents, and cover operating costs through growth in submissions and publications. The goal is to make literature more useful to scientists and the public.
Of CUNY, By CUNY, For CUNY: How Open Access Can Benefit Everyone at CUNY (and...Jill Cirasella
CUNY would greatly benefit from open access to scholarly works. An institutional repository at CUNY could make faculty research more accessible and increase its impact, while benefiting students and libraries. Many funding agencies and universities support open access policies. CUNY establishing its own institutional repository would make it easier for faculty to share their works openly through green open access self-archiving.
This document discusses visualizing genomic variation from DNA sequencing data. It begins by defining genomic variation such as single nucleotide polymorphisms and structural variations. It then discusses analyzing multiple samples, showing affected genes and clustering individuals. The document outlines challenges in visualizing high-dimensional genomic data from deep sequencing at scale, while maintaining computational performance for interactivity. It proposes representing rearranged chromosomes based on segment relationships to focus on functional impacts.
Visual Analytics in Omics - why, what, how?Jan Aerts
This document discusses visual analytics in omics data. It begins by noting the shift from hypothesis-driven to data-driven research due to large datasets. Visual analytics can help explore these data by opening the "black box" of algorithms and enabling researchers to develop hypotheses. Effective visualization leverages human perception through techniques like preattentive vision and Gestalt laws. Challenges to visual analytics include scalability issues for large datasets and identifying interesting patterns for further analysis. Examples demonstrate data exploration, filtering, and user-guided analysis in genomic applications.
Opening up Scientific and Scholarly CommunicationJonathan Eisen
The document discusses the history and goals of the Public Library of Science (PLoS), an organization founded in 2000 to promote open access scientific publishing. PLoS circulated an open letter calling for freely accessible scientific literature and launched their own open access journals, PLoS Biology and PLoS Medicine, after not enough publishers supported open access. The document also describes the author's personal experience with lack of access to scientific papers delaying treatment for his stillborn son, which reinforced his views that limiting access is unethical and counterproductive to advancing scientific knowledge.
PLOS (Public Library of Science) is a nonprofit open-access publisher founded in 2001 with a mission to accelerate scientific progress. PLOS makes research articles immediately and freely available worldwide under open-access licenses. It publishes several peer-reviewed journals covering various scientific fields like biology, medicine, and genetics. PLOS advocates for openness in science through open data sharing, transparent peer review processes, and making research outputs openly accessible for all.
Opening up to Diversity talk by @phylogenomics at #UCDPHSAJonathan Eisen
This document summarizes the key points of an article on the diversity and composition of bacteria in indoor environments. It finds that the bacterial communities found indoors are less diverse than outdoors, and that mechanically ventilated rooms contain less diverse communities than window ventilated rooms. Certain building attributes like ventilation source, airflow rates, humidity and temperature are correlated with the diversity and types of bacteria present. Rooms with lower airflow and humidity have higher abundances of potential human pathogens. The study suggests that building design and operation can manage the indoor microbiome and species that may colonize the human microbiome.
Presentation given at Open Science question and answer session hosted by the Institute for Quantitative Social Science (IQSS), and the Office for Scholarly Communication (OSC) at Harvard University, on July 16th 2014.
Bringing the Social Media Revolution to Thoracic SurgeryMayo Clinic
The document discusses bringing social media to thoracic surgery and the AATS 2013 annual meeting. It provides details on the scientific program, guest lectures, and social events at the meeting. It also describes the objectives and activities of the Mayo Clinic Center for Social Media, including their work to promote the use of social media in healthcare. Finally, it discusses Lee Aase's background and objectives for the webinar on applying social media in clinical practice, education, and research.
Open Data and Open Science presented in Rio for Open Science 2014-08-22. I argue that Open Notebook Science is the way forward and will lead to great benefits
The document discusses the potential for open science and data to disrupt traditional academic institutions by deinstitutionalizing rewards and metrics for scientific research. It argues that fully embracing open practices like data sharing, collaboration and publishing in open access venues is necessary for a more transparent and reproducible scientific process, but that many academic institutions have yet to adapt their reward systems to incentivize these activities. The talk outlines steps the scientific community can take to further this transition, such as developing community resources and standards, educating peers, and recognizing the different roles that institutions need to play to support open scholarship.
The document discusses several researchers' views on open access publishing. It summarizes that the researchers believe research funded by public money should be accessible to the public, open access removes barriers to research, and that it builds research capacity globally. However, some note that open access publishing costs can be high.
- Research results should be accessible to the public. The outputs of research funded by public money should serve the general public.
- Open access removes barriers to accessing research outcomes and promotes sharing of scientific knowledge. It also helps build research capacity in developing countries by providing access to journals.
- Open access publishing can have benefits like higher citation rates for articles and allowing broader access to research. However, page charges to publish open access can be expensive.
This document summarizes a digital natives seminar about open access publishing and predatory journals. It discusses rising journal prices, copyright issues for faculty publishing work, different types of open access like gold and green open access. It describes benefits and issues with open access like identifying predatory journals. It provides resources for evaluating journals and understanding publisher policies on self-archiving. It introduces the institutional repository Constellation that Benedictine University uses to provide open access to scholarly works.
This document summarizes a digital natives seminar about open access publishing and predatory journals. It discusses rising journal prices, copyright issues for faculty publishing work, different types of open access like gold and green open access. It describes benefits and issues with open access like identifying predatory journals. It provides resources for evaluating journals and understanding publisher policies on self-archiving. It introduces the institutional repository Constellation that Benedictine University uses to provide open access to scholarly works.
This document summarizes a digital natives seminar about open access publishing and predatory journals. It discusses rising journal prices, copyright issues for faculty publishing work, different types of open access like gold and green open access. It describes benefits and issues with open access like identifying predatory journals. It provides resources for evaluating journals and understanding publisher policies on self-archiving. It introduces the institutional repository Constellation that Benedictine University uses to provide open access to scholarly works.
Scholarly communication: Not just for scholars anymoreJoseph Kraus
This document discusses scholarly communication and open access. It notes that while various organizations push for more open access to research, there are still misunderstandings about open access among scientists, researchers, publishers and librarians. Specifically, some misunderstand behaviors include thinking open access is not needed or that the general public would not understand research articles. The document also discusses how the culture among scientists values traditional peer-reviewed journals and gatekeepers, and is slow to change. It suggests librarians can help address these issues by continuing to observe scientist behaviors and demonstrating the benefits of open access, such as increased citations.
Tina Baich, IUPUI University Library, USA Diminishing the perceived need f...CTLes
This document discusses diminishing unauthorized or "black" open access sharing. It begins with an overview of open access models and levels of black open access from oblivious offenders to hijackers. It then discusses discovery tools like OAB and Unpaywall and a library action plan focusing on improved discovery and delivery integration, educating users, and collection strategies emphasizing open access. The goal is to steer users towards legal options while understanding motivations for unauthorized sharing and how libraries can help meet user needs.
Rethinking the Functions of a Journal - some case studies from PLoS by Mark P...dduin
The document discusses re-engineering scientific journals to better serve their functions of registration, certification, dissemination and preservation. It describes PLoS's efforts to make scientific literature openly accessible online through journals like PLoS Biology and PLoS Medicine. PLoS is working to improve the organization of content by topic and impact, speed up authoring and certification through approaches like PLoS Currents, and cover operating costs through growth in submissions and publications. The goal is to make literature more useful to scientists and the public.
Of CUNY, By CUNY, For CUNY: How Open Access Can Benefit Everyone at CUNY (and...Jill Cirasella
CUNY would greatly benefit from open access to scholarly works. An institutional repository at CUNY could make faculty research more accessible and increase its impact, while benefiting students and libraries. Many funding agencies and universities support open access policies. CUNY establishing its own institutional repository would make it easier for faculty to share their works openly through green open access self-archiving.
This document discusses visualizing genomic variation from DNA sequencing data. It begins by defining genomic variation such as single nucleotide polymorphisms and structural variations. It then discusses analyzing multiple samples, showing affected genes and clustering individuals. The document outlines challenges in visualizing high-dimensional genomic data from deep sequencing at scale, while maintaining computational performance for interactivity. It proposes representing rearranged chromosomes based on segment relationships to focus on functional impacts.
Visual Analytics in Omics - why, what, how?Jan Aerts
This document discusses visual analytics in omics data. It begins by noting the shift from hypothesis-driven to data-driven research due to large datasets. Visual analytics can help explore these data by opening the "black box" of algorithms and enabling researchers to develop hypotheses. Effective visualization leverages human perception through techniques like preattentive vision and Gestalt laws. Challenges to visual analytics include scalability issues for large datasets and identifying interesting patterns for further analysis. Examples demonstrate data exploration, filtering, and user-guided analysis in genomic applications.
Visual Analytics in Omics: why, what, how?Jan Aerts
Visual Analytics in omics can help address several challenges in analyzing complex biological data:
- It allows researchers to explore large datasets in an interactive way to generate hypotheses, as the initial analysis is often exploratory rather than driven by a specific hypothesis.
- It opens the "black box" of automated analysis by making the analysis process transparent and understandable to domain experts.
- Effective visualization techniques leverage human visual perception and cognition to facilitate reasoning about the data.
This document discusses the shift from hypothesis-driven to data-driven scientific research paradigms and the role of visualization in facilitating human reasoning about complex data. It describes visualization as a framework involving interaction, visual representations, and analytics to support biological data exploration and hypothesis generation. Examples are provided of visualization tools that enable interactive analysis, algorithm development by making black boxes transparent, and user-guided analysis through continuous refinement. Challenges in scalability, uncertainty, evaluation and infrastructure are also discussed.
Visualizing the Structural Variome (VMLS-Eurovis 2013)Jan Aerts
This document discusses visualizing structural variation in genomes. It begins by defining structural variation and copy number variation. It then discusses why structural variation is important, listing examples of traits influenced by copy number differences. The document outlines challenges in visualizing structural variation data from techniques like array CGH and sequencing. It proposes dual approaches - focusing on functional impact and representing rearranged chromosomes based on segment relationships. Future directions discussed include single-cell analysis and cross-omic data integration.
The document discusses humanizing data analysis by putting the human back in the loop of data analysis processes. It notes that current data analysis involves filtering and other automated tasks that act as a "black box" for humans. The author argues that data analysis should involve generating hypotheses with the human perspective in mind through techniques like visual analytics and cognitive tasks to make the data analysis process more transparent and understandable for people.
This document provides an introduction to data visualization. It discusses what data visualization is, why it is used, and the stages involved in creating visualizations from data. Key points include:
- Data visualization involves using visual representations of data to help people analyze and communicate information more effectively.
- Visualizations are used for tasks like recording information, analyzing data to support reasoning, and communicating information.
- The process of creating visualizations involves understanding the properties of the data, properties of images and perception, and rules for mapping data to visual encodings.
- Important considerations include which visual variables to use to encode different data properties, principles of visual perception, and enabling interaction with the data. Validation of the effectiveness of
L Fu - Dao: a novel programming language for bioinformaticsJan Aerts
The document introduces Dao, a new programming language for bioinformatics. It discusses Dao's key features like optional typing, native support for concurrent programming, an LLVM-based JIT compiler, simple C interfaces, and the ClangDao tool for wrapping C/C++ libraries. An example demonstrates using thread tasks and futures for concurrent programming. The document outlines future plans to develop BioDao, an open source project providing bioinformatics modules to the Dao language.
J Wang - bioKepler: a comprehensive bioinformatics scientific workflow module...Jan Aerts
Presentation at BOSC2012 by J Wang - bioKepler: a comprehensive bioinformatics scientific workflow module for distributed analysis of large-scale biological data
B Temperton - The Bioinformatics Testing ConsortiumJan Aerts
The Bioinformatics Testing Consortium aims to improve bioinformatics software by having software tested by others in addition to the developers. It will assign testers to review open source bioinformatics projects and ensure they meet minimum standards through running standard tests and verifying output matches test data. This benefits new users by providing more reliable software, developers by identifying bugs, testers by learning quality standards, and journal editors by ensuring published software is fit for purpose. The consortium seeks feedback, participation, test cases, and engagement on Twitter to achieve its goals.
J Goecks - The Galaxy Visual Analysis FrameworkJan Aerts
The document describes Galaxy, an open-source web-based platform for visual analysis of genomic data. Galaxy provides tools for obtaining, integrating, analyzing, visualizing, sharing and publishing complete genomic analyses through a graphical user interface. It allows users to easily chain tools and create complex analysis workflows. The document highlights several Galaxy visualization tools, including Trackster for interactive exploration of large genomic datasets, Paramamonster for parameter space exploration, and Circster for circular genome-wide views. Future directions include expanding visualization capabilities to other data types and integrating multiple coordinated views.
GMOD in the Cloud provides preinstalled GMOD tools like Tripal, Chado, GBrowse, and JBrowse on cloud.gmod.org. These tools allow users to visualize, annotate, and manage biological data in the cloud. Potential use cases include community annotation events where users can load data, configure tools, annotate, and then export annotations without installing software locally. Using the cloud avoids installation issues and saves money while providing access to sample genomic datasets.
B Chapman - Toolkit for variation comparison and analysisJan Aerts
The document describes a toolkit for comparing variant calls from different variant callers and sequencing technologies. It proposes establishing a set of true variants by comparing calls across multiple callers and technologies on gold standard genomes. The toolkit includes a comparison architecture that analyzes variants, identifies real variants by summarizing metrics, and scales to large numbers of variants and samples. It also describes building analysis pipelines in Clojure and providing comparison results through a web interface with metrics. The goal is to help answer biological questions by determining true variants and prioritizing based on existing evidence.
J Klein - KUPKB: sharing, connecting and exposing kidney and urinary knowledg...Jan Aerts
The KUPKB integrates thousands of kidney and urinary pathway studies into an RDF knowledge base using ontologies to provide schema and annotation. The iKUP browser exposes the knowledge in a simple web interface, allowing biologists to more easily survey biological publications and generate hypotheses than traditional literature searches. The tools and APIs used make it possible to build such applications at relatively low cost.
A Kalderimis - InterMine: Embeddable datamining componentsJan Aerts
InterMine is an integrated data warehouse with an optimizing query engine. It provides web services and embeddable widgets to make powerful data querying accessible to non-technical users. InterMine runs databases for various model organisms and is working to make machine-readable APIs and data displays universally accessible.
E Afgan - Zero to a bioinformatics analysis platform in four minutesJan Aerts
This document discusses how to quickly set up a bioinformatics analysis platform in four minutes using various open source tools. It introduces CloudBioLinux for building custom tool suites, CloudMan for creating scalable processing platforms, Galaxy for exploratory analysis, and BioCloudCentral for getting started easily. A new Python library called Blend is also introduced for automating repetitive tasks related to analysis and infrastructure manipulation using the APIs of these tools.
B Kinoshita - Creating biology pipelines with BioUnoJan Aerts
BioUno is an open source project that uses continuous integration tools like Jenkins to create biology pipelines. It was created by Bruno Kinoshita in Brazil as a way to apply DevOps practices to biology. BioUno uses Jenkins for its jobs, notifications, and integration with other tools. The next steps are to enhance documentation, find new developers and users, and compare BioUno to other similar biology tools.
The document discusses updates to the Galaxy API and automatic parallelization capabilities. The RESTful Galaxy API now uses JSON and authentication keys instead of usernames/passwords. Tools can be configured for automatic parallelization to take advantage of available resources. The Tool Shed allows simple installation and updating of tools and workflows in a Galaxy instance.
Enchancing adoption of Open Source Libraries. A case study on Albumentations.AIVladimir Iglovikov, Ph.D.
Presented by Vladimir Iglovikov:
- https://www.linkedin.com/in/iglovikov/
- https://x.com/viglovikov
- https://www.instagram.com/ternaus/
This presentation delves into the journey of Albumentations.ai, a highly successful open-source library for data augmentation.
Created out of a necessity for superior performance in Kaggle competitions, Albumentations has grown to become a widely used tool among data scientists and machine learning practitioners.
This case study covers various aspects, including:
People: The contributors and community that have supported Albumentations.
Metrics: The success indicators such as downloads, daily active users, GitHub stars, and financial contributions.
Challenges: The hurdles in monetizing open-source projects and measuring user engagement.
Development Practices: Best practices for creating, maintaining, and scaling open-source libraries, including code hygiene, CI/CD, and fast iteration.
Community Building: Strategies for making adoption easy, iterating quickly, and fostering a vibrant, engaged community.
Marketing: Both online and offline marketing tactics, focusing on real, impactful interactions and collaborations.
Mental Health: Maintaining balance and not feeling pressured by user demands.
Key insights include the importance of automation, making the adoption process seamless, and leveraging offline interactions for marketing. The presentation also emphasizes the need for continuous small improvements and building a friendly, inclusive community that contributes to the project's growth.
Vladimir Iglovikov brings his extensive experience as a Kaggle Grandmaster, ex-Staff ML Engineer at Lyft, sharing valuable lessons and practical advice for anyone looking to enhance the adoption of their open-source projects.
Explore more about Albumentations and join the community at:
GitHub: https://github.com/albumentations-team/albumentations
Website: https://albumentations.ai/
LinkedIn: https://www.linkedin.com/company/100504475
Twitter: https://x.com/albumentations
Let's Integrate MuleSoft RPA, COMPOSER, APM with AWS IDP along with Slackshyamraj55
Discover the seamless integration of RPA (Robotic Process Automation), COMPOSER, and APM with AWS IDP enhanced with Slack notifications. Explore how these technologies converge to streamline workflows, optimize performance, and ensure secure access, all while leveraging the power of AWS IDP and real-time communication via Slack notifications.
Unlock the Future of Search with MongoDB Atlas_ Vector Search Unleashed.pdfMalak Abu Hammad
Discover how MongoDB Atlas and vector search technology can revolutionize your application's search capabilities. This comprehensive presentation covers:
* What is Vector Search?
* Importance and benefits of vector search
* Practical use cases across various industries
* Step-by-step implementation guide
* Live demos with code snippets
* Enhancing LLM capabilities with vector search
* Best practices and optimization strategies
Perfect for developers, AI enthusiasts, and tech leaders. Learn how to leverage MongoDB Atlas to deliver highly relevant, context-aware search results, transforming your data retrieval process. Stay ahead in tech innovation and maximize the potential of your applications.
#MongoDB #VectorSearch #AI #SemanticSearch #TechInnovation #DataScience #LLM #MachineLearning #SearchTechnology
For the full video of this presentation, please visit: https://www.edge-ai-vision.com/2024/06/building-and-scaling-ai-applications-with-the-nx-ai-manager-a-presentation-from-network-optix/
Robin van Emden, Senior Director of Data Science at Network Optix, presents the “Building and Scaling AI Applications with the Nx AI Manager,” tutorial at the May 2024 Embedded Vision Summit.
In this presentation, van Emden covers the basics of scaling edge AI solutions using the Nx tool kit. He emphasizes the process of developing AI models and deploying them globally. He also showcases the conversion of AI models and the creation of effective edge AI pipelines, with a focus on pre-processing, model conversion, selecting the appropriate inference engine for the target hardware and post-processing.
van Emden shows how Nx can simplify the developer’s life and facilitate a rapid transition from concept to production-ready applications.He provides valuable insights into developing scalable and efficient edge AI solutions, with a strong focus on practical implementation.
Sudheer Mechineni, Head of Application Frameworks, Standard Chartered Bank
Discover how Standard Chartered Bank harnessed the power of Neo4j to transform complex data access challenges into a dynamic, scalable graph database solution. This keynote will cover their journey from initial adoption to deploying a fully automated, enterprise-grade causal cluster, highlighting key strategies for modelling organisational changes and ensuring robust disaster recovery. Learn how these innovations have not only enhanced Standard Chartered Bank’s data infrastructure but also positioned them as pioneers in the banking sector’s adoption of graph technology.
Alt. GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using ...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
Removing Uninteresting Bytes in Software FuzzingAftab Hussain
Imagine a world where software fuzzing, the process of mutating bytes in test seeds to uncover hidden and erroneous program behaviors, becomes faster and more effective. A lot depends on the initial seeds, which can significantly dictate the trajectory of a fuzzing campaign, particularly in terms of how long it takes to uncover interesting behaviour in your code. We introduce DIAR, a technique designed to speedup fuzzing campaigns by pinpointing and eliminating those uninteresting bytes in the seeds. Picture this: instead of wasting valuable resources on meaningless mutations in large, bloated seeds, DIAR removes the unnecessary bytes, streamlining the entire process.
In this work, we equipped AFL, a popular fuzzer, with DIAR and examined two critical Linux libraries -- Libxml's xmllint, a tool for parsing xml documents, and Binutil's readelf, an essential debugging and security analysis command-line tool used to display detailed information about ELF (Executable and Linkable Format). Our preliminary results show that AFL+DIAR does not only discover new paths more quickly but also achieves higher coverage overall. This work thus showcases how starting with lean and optimized seeds can lead to faster, more comprehensive fuzzing campaigns -- and DIAR helps you find such seeds.
- These are slides of the talk given at IEEE International Conference on Software Testing Verification and Validation Workshop, ICSTW 2022.
Full-RAG: A modern architecture for hyper-personalizationZilliz
Mike Del Balso, CEO & Co-Founder at Tecton, presents "Full RAG," a novel approach to AI recommendation systems, aiming to push beyond the limitations of traditional models through a deep integration of contextual insights and real-time data, leveraging the Retrieval-Augmented Generation architecture. This talk will outline Full RAG's potential to significantly enhance personalization, address engineering challenges such as data management and model training, and introduce data enrichment with reranking as a key solution. Attendees will gain crucial insights into the importance of hyperpersonalization in AI, the capabilities of Full RAG for advanced personalization, and strategies for managing complex data integrations for deploying cutting-edge AI solutions.
Maruthi Prithivirajan, Head of ASEAN & IN Solution Architecture, Neo4j
Get an inside look at the latest Neo4j innovations that enable relationship-driven intelligence at scale. Learn more about the newest cloud integrations and product enhancements that make Neo4j an essential choice for developers building apps with interconnected data and generative AI.
TrustArc Webinar - 2024 Global Privacy SurveyTrustArc
How does your privacy program stack up against your peers? What challenges are privacy teams tackling and prioritizing in 2024?
In the fifth annual Global Privacy Benchmarks Survey, we asked over 1,800 global privacy professionals and business executives to share their perspectives on the current state of privacy inside and outside of their organizations. This year’s report focused on emerging areas of importance for privacy and compliance professionals, including considerations and implications of Artificial Intelligence (AI) technologies, building brand trust, and different approaches for achieving higher privacy competence scores.
See how organizational priorities and strategic approaches to data security and privacy are evolving around the globe.
This webinar will review:
- The top 10 privacy insights from the fifth annual Global Privacy Benchmarks Survey
- The top challenges for privacy leaders, practitioners, and organizations in 2024
- Key themes to consider in developing and maintaining your privacy program
Unlocking Productivity: Leveraging the Potential of Copilot in Microsoft 365, a presentation by Christoforos Vlachos, Senior Solutions Manager – Modern Workplace, Uni Systems
A tale of scale & speed: How the US Navy is enabling software delivery from l...sonjaschweigert1
Rapid and secure feature delivery is a goal across every application team and every branch of the DoD. The Navy’s DevSecOps platform, Party Barge, has achieved:
- Reduction in onboarding time from 5 weeks to 1 day
- Improved developer experience and productivity through actionable findings and reduction of false positives
- Maintenance of superior security standards and inherent policy enforcement with Authorization to Operate (ATO)
Development teams can ship efficiently and ensure applications are cyber ready for Navy Authorizing Officials (AOs). In this webinar, Sigma Defense and Anchore will give attendees a look behind the scenes and demo secure pipeline automation and security artifacts that speed up application ATO and time to production.
We will cover:
- How to remove silos in DevSecOps
- How to build efficient development pipeline roles and component templates
- How to deliver security artifacts that matter for ATO’s (SBOMs, vulnerability reports, and policy evidence)
- How to streamline operations with automated policy checks on container images
Why You Should Replace Windows 11 with Nitrux Linux 3.5.0 for enhanced perfor...SOFTTECHHUB
The choice of an operating system plays a pivotal role in shaping our computing experience. For decades, Microsoft's Windows has dominated the market, offering a familiar and widely adopted platform for personal and professional use. However, as technological advancements continue to push the boundaries of innovation, alternative operating systems have emerged, challenging the status quo and offering users a fresh perspective on computing.
One such alternative that has garnered significant attention and acclaim is Nitrux Linux 3.5.0, a sleek, powerful, and user-friendly Linux distribution that promises to redefine the way we interact with our devices. With its focus on performance, security, and customization, Nitrux Linux presents a compelling case for those seeking to break free from the constraints of proprietary software and embrace the freedom and flexibility of open-source computing.
“An Outlook of the Ongoing and Future Relationship between Blockchain Technologies and Process-aware Information Systems.” Invited talk at the joint workshop on Blockchain for Information Systems (BC4IS) and Blockchain for Trusted Data Sharing (B4TDS), co-located with with the 36th International Conference on Advanced Information Systems Engineering (CAiSE), 3 June 2024, Limassol, Cyprus.
1. Science Wants to Be Open:
If Only We Could Get Out of Its Way
BOSC2012
July 12, 2012
Jonathan A. Eisen
University of California, Davis
@phylogenomics
Friday, July 13, 12
4. Public Library of Science (PLoS)
• Started in 2000 by
•Harold Varmus
•Pat Brown
•Michael Eisen
• First action was to circulate an
open letter on publishing
Friday, July 13, 12
5. The Letter
We support the establishment of an online public library that would
provide the full contents of the published record of research and scholarly
discourse in medicine and the life sciences in a freely accessible, fully
searchable, interlinked form. Establishment of this public library would vastly
increase the accessibility and utility of the scientific literature, enhance
scientific productivity, and catalyze integration of the disparate communities of
knowledge and ideas in biomedical sciences.We recognize that the publishers
of our scientific journals have a legitimate right to a fair financial return for
their role in scientific communication. We believe, however, that the
permanent, archival record of scientific research and ideas should neither be
owned nor controlled by publishers, but should belong to the public and should
be freely available through an international online public library.To encourage
the publishers of our journals to support this endeavor, we pledge that,
beginning in September 2001, we will publish in, edit or review for, and
personally subscribe to only those scholarly and scientific journals
that have agreed to grant unrestricted free distribution rights to any
and all original research reports that they have published, through PubMed
Central and similar online public resources, within 6 months of their initial
publication date.
Friday, July 13, 12
6. The Letter
We support the establishment of an online public library that would
provide the full contents of the published record of research and scholarly
discourse in medicine and the life sciences in a freely accessible, fully
searchable, interlinked form. Establishment of this public library would vastly
increase the accessibility and utility of the scientific literature, enhance
scientific productivity, and catalyze integration of the disparate communities of
knowledge and ideas in biomedical sciences.We recognize that the publishers
of our scientific journals have a legitimate right to a fair financial return for
their role in scientific communication. We believe, however, that the
permanent, archival record of scientific research and ideas should neither be
owned nor controlled by publishers, but should belong to the public and should
be freely available through an international online public library.To encourage
the publishers of our journals to support this endeavor, we pledge that,
beginning in September 2001, we will publish in, edit or review for, and
personally subscribe to only those scholarly and scientific journals
that have agreed to grant unrestricted free distribution rights to any
and all original research reports that they have published, through PubMed
Central and similar online public resources, within 6 months of their initial
publication date.
Friday, July 13, 12
9. J-
Can you get people to sign this and FAX it to me.
1-786-549-0137. Craig and
Claires sigs would be greatly appreciated.
I assume I can put your name on it, no?
I set up a site http://www.publiclibraryofscience.org
to keep lists of
people who have signed.
-M
Friday, July 13, 12
10. PLoS After the Letter (2003)
• > 25,000 people signed the letter
• Small increase in open access
support
• But not enough
• So PLoS announced the launch of
their own journals
•PLoS Biology
•PLoS Medicine
Friday, July 13, 12
11. Me and PLoS
• Joined founding
Editorial Board of
PLoS Biology
• Still not fully
convinced about
need for OA
• Worried more about
User agrees to push for full “Open
not publish Science”
genome level
analyses
Friday, July 13, 12
12. Ft. Lauderdale Agreement
• Feb 2003 meeting in Ft. Lauderdale on “Genome
Sequencing Data Release Policies”
• Follow up to the “Bermuda Accord”
• Debate about how open to be with data
• NHGRI had supported a similar policy to TIGRs
(see http://www.genome.gov/10506537)
• Sean Eddy gave a talk that convinced me that
these restrictions we in direct conflict with the
whole point of giving money to places to generate
the data
• So I did what any scientist should do - some
experiments
Friday, July 13, 12
13. Open Data Experiment
• Unrestricted data
access policy on
Tetrahymena thermophila
• First time done at
TIGR
• Many people
published papers
before we did
• But many more helped
with our paper
1 The Institute for Genomic Research, Rockville, Maryland, United States of America, 2 Department
of Biology, York University, Toronto, Ontario, Canada, 3 Centre for Research in Mass Spectrometry,
York University, Toronto, Ontario, Canada, 4 Department of Biological Sciences, Marquette
University, Milwaukee, Wisconsin, United States of America, 5 Razavi-Newman Center for
Thanks for the message about the
Bioinformatics, The Salk Institute for Biological Studies, San Diego, California, United States of
America, 6 Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago,
Illinois, United States of America, 7 Department of Biology, Harvey Mudd College, Claremont,
genome, that is a nice surprise. Lots of
California, United States of America, 8 Department of Biology, University of Texas at San Antonio,
San Antonio, Texas, United States of America, 9 Department of Electrical Engineering, University of
Texas at San Antonio, San Antonio, Texas, United States of America, 10 Department of Molecular
and Cellular Biology, University of California Berkeley, Berkeley, California, United States of America,
Bacillus DNA in there unfortunately but
11 Department of Computer Science and Engineering, University of Washington, Seattle,
Washington, United States of America, 12 Department of Cellular Biology, University of Georgia,
Athens, Georgia, United States of America, 13 Department of Biological Sciences, University of
we are going to go wild looking in it.
Iowa, Iowa City, Iowa, United States of America, 14 Department of Biology, University of Rochester,
Rochester, New York, United States of America, 15 Canadian Institute for Advanced Research,
Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada, 16
Department of Genetics, Stanford University, Stanford, California, United States of America, 17
Department of Molecular, Cellular, and Developmental Biology, University of California Santa
Barbara, Santa Barbara, California, United States of America Patrick
Friday, July 13, 12
14. Open Access Experiment
• Had published one paper in an
Open Access journal (Genome
Biology)
• We were working on a paper on
WMD - the the first Wolbachia genome
Wolbachia of
Male • Wolbachia are maternally
transmitted parasites that target
Destruction males in many species
• In filarial nematodes appear to
be mutualistic symbionts
• Our paper was being recruited
by Nature and Science
Friday, July 13, 12
17. Experiments in Progress …
• But still unclear to me whether this Open
Access thing was a good idea or not
• Then real life intervened
Friday, July 13, 12
19. Lack of Access
• Scientist without access
• Would access have helped?
• Is limiting access useful or needed?
• Goal of much of scientific and medical
research is to spread knowledge
Friday, July 13, 12
23. Open Access
• Free, immediate access online
Unrestricted distribution and re-use
Author retains rights to attribution
Papers are immediately deposited in a
public online archive, such as PubMed Central
Bethesda Principles, April 2003
Friday, July 13, 12
24. Open Access
• Free, immediate access online
Unrestricted distribution and re-use
Author retains rights to attribution
Papers are immediately deposited in a
public online archive, such as PubMed Central
Bethesda Principles, April 2003
Friday, July 13, 12
29. Search BRCA1 human
You can purchase online access to this
article (and all its versions) for a 24-
hour period. Articles are US $ 29.95,
with some exceptions where prices may
vary. Click "Buy Now" to display the
price
Friday, July 13, 12
34. Blast Result
You can purchase online access to this
article (and all its versions) for a 24-
hour period. Articles are US $ 29.95,
with some exceptions where prices may
vary. Click "Buy Now" to display the
price
Friday, July 13, 12
35. Blast Result
Plus - you are not allowed to share your
alignments with anyone
Friday, July 13, 12
37. A network of literature and data
Friday, July 13, 12
38. A network of literature and data
Free = you can read all the papers
Friday, July 13, 12
39. A network of literature and data
Open = Repurpose and share any
part of your analysis w/ no
restrictions. No lawyers. No fear.
Friday, July 13, 12
40. Educational Benefits of OA
• No debate about “fair use”
• No need for password’s or logins for
course web sites
• No lawyers have to be involved
• Material from OA publications can be
repackaged for any purpose
Friday, July 13, 12
41. Many Exiting Barriers
• Impact factor
• Money raising efforts
• Conservative behaviors
• Red herrings
• Lack of peer review
• Cost of publishing
• Journal copyright protects authors
• Lobbyists
Friday, July 13, 12
42. Other Areas of Open Science
• Open data
• Open source software
• Open discussion
• Open resources
• Open review
Friday, July 13, 12