Pathema Website Functionality Enhancements

•

0 likes•600 views

Pathema

Conference: Annual BRC Meeting (BRC6), Oct 28-29, 2008 in Ft. Lauderedale, Florida. Presenter: Tanja Davidsen

Technology

Pathema Website Functionality
Enhancements:
Pathema gets its Sexy Back

Tanja Davidsen, Ph.D.
J. Craig Venter Institute

Improved Searches using Lucene

• Improved speed and functionality of the search queries
on Pathema
• An open source information retrieval library supported by
Apache
• At the core of the Lucene logical architecture is a
document containing fields of text, independent of file
format
• Prevents us from hitting the database for searches,
especially helpful for inexact searches
• Used by Wikipedia, Monster, SourceForge, UniProt and
EBI

Improved Searches using Lucene

• Improves our search speed from 30+s to 1-3s
• Filters will allow us to let the users build even
more complex queries:
Search for all genes in organism B.anthracis starting


with the “dna” and assigned GO ID GO:0003677

GBrowse (GMOD)

• The most popular GMOD viewer
• Used to replace and/or accompany our in
house genome viewers
• Order and appearance of tracks are
customizable by administrator and end-user
• Supports third party annotation using GFF
formats
• Third-party feature loading
• Customizable plug-in architecture (e.g. run
BLAST, find oligonucleotides, design
primers)

ClosTox: The Clostridum Toxin DB

• The Clostridium community is primarily
interested in the toxin genes
• We created a specialty toxin and neurotoxin
associated proteins (NAPs) database for
browsing on the Clostridium site
• Data for the database provided by Clostridium
researchers/community
• Very successful debut at the last Botulism
meeting

Sybil: Comparative Genomic Region

• Compares a reference to selected
comparison genomes by protein clusters
• Specify how many clustered genes a non-
reference sequence region must have in
common to with the reference

Sybil: Synteny gradient display
• A color-coded display of conserved synteny
between two or more sequences
• Select a reference sequence (bottom of the
display) with the genes color-coded from the 5’
end to the 3’ end
• Orthologs in the comparison genomes are
shown in the color of the ortholog from the
reference genome
• As a result one can see large and small-scale
rearrangements at a glance, in addition to
regions that may be inserted in one sequence
relative to another

New Data Types

• Virulence Factors
• Epitopes
• Experimentally characterized
genes/proteins
• Multidrug transporters
• Genomic islands
• Community requested databases
(ClosTox)

Acknowledgements

• PI: Granger Sutton (JCVI)
• Subcontract: Owen White (University of Maryland, Baltimore, IGS)
• Project Manager: Lauren Brinkac

JCVI Informatics Engineers Analysts


Tanja Davidsen (manager) Scott Durkin (manager)


Erin Beck Ramana Madupu


Alex Richter Susmita Shrivastava


Kevin Galinsky Bob Dodson


Jay Sundaram Derek Harkins


Seth Schobel Lis Caler


IGS Informatics Engineers


Anu Ganapathy YongMei Zhao


Josh Orvis Aaron Gussman


Kevin Galens Jonathon Crabtree


KnetMiner, with a silent "K" and standing for Knowledge Network Miner, is a suite of open-source software tools developed at Rothamsted Research for integrating and visualising large biological datasets in order to accelerate gene discovery. The software mines the myriad databases that describe an organism’s biology to present links between relevant pieces of information, such as genes, biological pathways, phenotypes or publications. The aim is to provide leads for scientists who are investigating the molecular basis for a particular trait or ways of improving the organism’s performance in some way

Cloud bioinformatics 2

ARPUTHA SELVARAJ A

Arraygen_BrochureDeepak Pathak

Implementation of GPU-based bioinformatic tools at the ENCODE DCC

ENCODE-DCC

Mar2013 Performance Metrics Working GroupGenomeInABottle

Final Acb All Hands 26 11 07.Key

guest3d0531

Genome annotation with open source software: Apollo, Jbrowse and the GO in Ga...

Nathan Dunn

Día 19 - Noel Chen - Introducción a Novogene

Alejandro Borges

TGAC Browser bosc 2014

Anil Thanki

Informal presentation on bioinformaticsAtai Rabby

Reproducible research - to infinity

PeterMorrell4

Giab for jax long read 190917

GenomeInABottle

Arraygen brochure

Rajesh Mahato

Cool Informatics Tools and Services for Biomedical ResearchDavid Ruau

Eln Jisc Mrc 18dec07 Nsb

Nicolas Bertrand

Next generation sequencing & microarray-- Genotypic Technology

Genotypic Technology

Greetings from Genotypic Technology, Bangalore (www.genotypic.co.in). We are a 13 year old genomics and bioinformatics company ( 65+ employees, Service. Products and R & D) based in Bangalore, India, primarily working on applications of Microarrays and Next Generation Sequencing in Human Health and Disease, including in Molecular Diagnostics, Prognosis, Therapeutics, Vaccine Research, Basic Science Research, Veterinary Science, Agriculture, Industrial Biotechnology, Microbial Genetics and more. Our major strength is in customized genomics solutions, particularly in your field, we can develop panel of markers for specific diseases, optimize, validate and help commercialize on open platforms or specific instrument platforms- in microarrays and sequencing based methods/ assays. We can also use genomic markers to aid in treatment of specific disease using personalized medicine approaches. All this can be done on a comprehensive end-to-end manner in our company as we have a very good blend of molecular biology and bioinformatics with totally 6 Ph.Ds. We work closely with Agilent's R &D as their partner.

Apollo: Scalable & collaborative curation of genomes - Biocuration 2015

Monica Munoz-Torres

Talk at the 8th International Biocuration Conference. Beijing, China. April 23-26, 2015. Obtaining meaningful results from genome analyses requires high quality annotations of all genomic elements. Today’s sequencing projects face challenges such as lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing curators to improve on existing automated gene models through an intuitive interface. Apollo’s extensible architecture is built on top of JBrowse; its components are a web-based client, an annotation-editing engine, and a server-side data service. It allows users to visualize automated gene models, protein alignments, expression and variant data, and conduct structural and/or functional annotations. Apollo is actively used within a variety of projects, including the initiative to sequence the genomes of 5,000 Arthropod species (i5K), and will become essential to the thousands of genomes now being sequenced and analyzed. Researchers from nearly 100 institutions worldwide are currently using Apollo on distributed curation efforts for over sixty genome projects across the tree of life; from plants to echinoderms, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog. We are training the next generation of researchers by reaching out to educators to make these tools available as part of curricula, offering workshops and webinars to the scientific community, and through widely applied systems such as iPlant and DNA Subway. We are currently integrating Apollo into an annotation environment combining gene structural and functional annotation, transcriptomic, proteomic, and phenotypic annotation. In this presentation we will describe in detail its utility to users, introduce the architecture to developers interested in expanding on this open-source project, and offer details of our future plans. Authors: Monica Munoz-Torres(1), Nathan Dunn(1), Colin Diesh(2), Deepak Unni(2), Seth Carbon(1), Heiko Dietze(1), Christopher Mungall(1), Nicole Washington(1), Ian Holmes(3), Christine Elsik(2), and Suzanna E. Lewis(1) 1Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, CA 2Divisions of Animal and Plant Sciences, University of Missouri, Columbia, MO 3University of California Berkeley, Bioengineering, Berkeley, CA

Pathema-Clostridium A NIAID Bioinformatics Resource Center (BRC)

Pathema

Pathema Burkholderia Annotation Jamboree: A Guide to MANATEE

Pathema

Similar to Pathema Website Functionality Enhancements

Ensembl annotation

Genome Reference Consortium

Kim Pruitt trainingbiocuration2015

Kim D. Pruitt

Making powerful science: an introduction to NGS data analysis

AdamCribbs1

KnetMiner Overview Oct 2017

Keywan Hassani-Pak

Cloud bioinformatics 2

ARPUTHA SELVARAJ A

Arraygen_BrochureDeepak Pathak

Implementation of GPU-based bioinformatic tools at the ENCODE DCC

ENCODE-DCC

Mar2013 Performance Metrics Working GroupGenomeInABottle

Final Acb All Hands 26 11 07.Key

guest3d0531

Genome annotation with open source software: Apollo, Jbrowse and the GO in Ga...

Nathan Dunn

Día 19 - Noel Chen - Introducción a Novogene

Alejandro Borges

TGAC Browser bosc 2014

Anil Thanki

Informal presentation on bioinformaticsAtai Rabby

Reproducible research - to infinity

PeterMorrell4

Giab for jax long read 190917

GenomeInABottle

Arraygen brochure

Rajesh Mahato

Cool Informatics Tools and Services for Biomedical ResearchDavid Ruau

Eln Jisc Mrc 18dec07 Nsb

Nicolas Bertrand

Next generation sequencing & microarray-- Genotypic Technology

Genotypic Technology

Apollo: Scalable & collaborative curation of genomes - Biocuration 2015

Monica Munoz-Torres

Similar to Pathema Website Functionality Enhancements (20)

Ensembl annotation

Kim Pruitt trainingbiocuration2015

Making powerful science: an introduction to NGS data analysis

KnetMiner Overview Oct 2017

Cloud bioinformatics 2

Arraygen_Brochure

Implementation of GPU-based bioinformatic tools at the ENCODE DCC

Mar2013 Performance Metrics Working Group

Final Acb All Hands 26 11 07.Key

Genome annotation with open source software: Apollo, Jbrowse and the GO in Ga...

Día 19 - Noel Chen - Introducción a Novogene

TGAC Browser bosc 2014

Informal presentation on bioinformatics

Reproducible research - to infinity

Giab for jax long read 190917

Arraygen brochure

Cool Informatics Tools and Services for Biomedical Research

Eln Jisc Mrc 18dec07 Nsb

Next generation sequencing & microarray-- Genotypic Technology

Apollo: Scalable & collaborative curation of genomes - Biocuration 2015

Recently uploaded

Epistemic Interaction - tuning interfaces to provide information for AI support

Alan Dix

Paper presented at SYNERGY workshop at AVI 2024, Genoa, Italy. 3rd June 2024 https://alandix.com/academic/papers/synergy2024-epistemic/ As machine learning integrates deeper into human-computer interactions, the concept of epistemic interaction emerges, aiming to refine these interactions to enhance system adaptability. This approach encourages minor, intentional adjustments in user behaviour to enrich the data available for system learning. This paper introduces epistemic interaction within the context of human-system communication, illustrating how deliberate interaction design can improve system understanding and adaptation. Through concrete examples, we demonstrate the potential of epistemic interaction to significantly advance human-computer interaction by leveraging intuitive human communication strategies to inform system design and functionality, offering a novel pathway for enriching user-system engagements.

FIDO Alliance Osaka Seminar: FIDO Security Aspects.pdf

FIDO Alliance

FIDO Alliance Osaka Seminar: Overview.pdf

FIDO Alliance

From Daily Decisions to Bottom Line: Connecting Product Work to Revenue by VP...

Product School

Essentials of Automations: Optimizing FME Workflows with Parameters

Safe Software

Are you looking to streamline your workflows and boost your projects’ efficiency? Do you find yourself searching for ways to add flexibility and control over your FME workflows? If so, you’re in the right place. Join us for an insightful dive into the world of FME parameters, a critical element in optimizing workflow efficiency. This webinar marks the beginning of our three-part “Essentials of Automation” series. This first webinar is designed to equip you with the knowledge and skills to utilize parameters effectively: enhancing the flexibility, maintainability, and user control of your FME projects. Here’s what you’ll gain: - Essentials of FME Parameters: Understand the pivotal role of parameters, including Reader/Writer, Transformer, User, and FME Flow categories. Discover how they are the key to unlocking automation and optimization within your workflows. - Practical Applications in FME Form: Delve into key user parameter types including choice, connections, and file URLs. Allow users to control how a workflow runs, making your workflows more reusable. Learn to import values and deliver the best user experience for your workflows while enhancing accuracy. - Optimization Strategies in FME Flow: Explore the creation and strategic deployment of parameters in FME Flow, including the use of deployment and geometry parameters, to maximize workflow efficiency. - Pro Tips for Success: Gain insights on parameterizing connections and leveraging new features like Conditional Visibility for clarity and simplicity. We’ll wrap up with a glimpse into future webinars, followed by a Q&A session to address your specific questions surrounding this topic. Don’t miss this opportunity to elevate your FME expertise and drive your projects to new heights of efficiency.

LF Energy Webinar: Electrical Grid Modelling and Simulation Through PowSyBl -...

DanBrown980551

Do you want to learn how to model and simulate an electrical network from scratch in under an hour? Then welcome to this PowSyBl workshop, hosted by Rte, the French Transmission System Operator (TSO)! During the webinar, you will discover the PowSyBl ecosystem as well as handle and study an electrical network through an interactive Python notebook. PowSyBl is an open source project hosted by LF Energy, which offers a comprehensive set of features for electrical grid modelling and simulation. Among other advanced features, PowSyBl provides: - A fully editable and extendable library for grid component modelling; - Visualization tools to display your network; - Grid simulation tools, such as power flows, security analyses (with or without remedial actions) and sensitivity analyses; The framework is mostly written in Java, with a Python binding so that Python developers can access PowSyBl functionalities as well. What you will learn during the webinar: - For beginners: discover PowSyBl's functionalities through a quick general presentation and the notebook, without needing any expert coding skills; - For advanced developers: master the skills to efficiently apply PowSyBl functionalities to your real-world scenarios.

Connector Corner: Automate dynamic content and events by pushing a button

DianaGray10

Here is something new! In our next Connector Corner webinar, we will demonstrate how you can use a single workflow to: Create a campaign using Mailchimp with merge tags/fields Send an interactive Slack channel message (using buttons) Have the message received by managers and peers along with a test email for review But there’s more: In a second workflow supporting the same use case, you’ll see: Your campaign sent to target colleagues for approval If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team But—if the “Reject” button is pushed, colleagues will be alerted via Slack message Join us to learn more about this new, human-in-the-loop capability, brought to you by Integration Service connectors. And... Speakers: Akshay Agnihotri, Product Manager Charlie Greenberg, Host

Assuring Contact Center Experiences for Your Customers With ThousandEyes

ThousandEyes

Mission to Decommission: Importance of Decommissioning Products to Increase E...

Product School

FIDO Alliance Osaka Seminar: The WebAuthn API and Discoverable Credentials.pdf

FIDO Alliance

UiPath Test Automation using UiPath Test Suite series, part 4

DianaGray10

Welcome to UiPath Test Automation using UiPath Test Suite series part 4. In this session, we will cover Test Manager overview along with SAP heatmap. The UiPath Test Manager overview with SAP heatmap webinar offers a concise yet comprehensive exploration of the role of a Test Manager within SAP environments, coupled with the utilization of heatmaps for effective testing strategies. Participants will gain insights into the responsibilities, challenges, and best practices associated with test management in SAP projects. Additionally, the webinar delves into the significance of heatmaps as a visual aid for identifying testing priorities, areas of risk, and resource allocation within SAP landscapes. Through this session, attendees can expect to enhance their understanding of test management principles while learning practical approaches to optimize testing processes in SAP environments using heatmap visualization techniques What will you get from this session? 1. Insights into SAP testing best practices 2. Heatmap utilization for testing 3. Optimization of testing processes 4. Demo Topics covered: Execution from the test manager Orchestrator execution result Defect reporting SAP heatmap example with demo Speaker: Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP

PCI PIN Basics Webinar from the Controlcase Team

ControlCase

Neuro-symbolic is not enough, we need neuro-*semantic*

Frank van Harmelen

Neuro-symbolic (NeSy) AI is on the rise. However, simply machine learning on just any symbolic structure is not sufficient to really harvest the gains of NeSy. These will only be gained when the symbolic structures have an actual semantics. I give an operational definition of semantics as “predictable inference”. All of this illustrated with link prediction over knowledge graphs, but the argument is general.

Dev Dives: Train smarter, not harder – active learning and UiPath LLMs for do...

UiPathCommunity

💥 Speed, accuracy, and scaling – discover the superpowers of GenAI in action with UiPath Document Understanding and Communications Mining™: See how to accelerate model training and optimize model performance with active learning Learn about the latest enhancements to out-of-the-box document processing – with little to no training required Get an exclusive demo of the new family of UiPath LLMs – GenAI models specialized for processing different types of documents and messages This is a hands-on session specifically designed for automation developers and AI enthusiasts seeking to enhance their knowledge in leveraging the latest intelligent document processing capabilities offered by UiPath. Speakers: 👨‍🏫 Andras Palfi, Senior Product Manager, UiPath 👩‍🏫 Lenka Dulovicova, Product Program Manager, UiPath

Encryption in Microsoft 365 - ExpertsLive Netherlands 2024

Albert Hoitingh

To Graph or Not to Graph Knowledge Graph Architectures and LLMs

Paul Groth

Securing your Kubernetes cluster_ a step-by-step guide to success !

KatiaHIMEUR1

Today, after several years of existence, an extremely active community and an ultra-dynamic ecosystem, Kubernetes has established itself as the de facto standard in container orchestration. Thanks to a wide range of managed services, it has never been so easy to set up a ready-to-use Kubernetes cluster. However, this ease of use means that the subject of security in Kubernetes is often left for later, or even neglected. This exposes companies to significant risks. In this talk, I'll show you step-by-step how to secure your Kubernetes cluster for greater peace of mind and reliability.

Smart TV Buyer Insights Survey 2024 by 91mobiles.pdf

91mobiles

State of ICS and IoT Cyber Threat Landscape Report 2024 preview

Prayukth K V

The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development. The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers: State of global ICS asset and network exposure Sectoral targets and attacks as well as the cost of ransom Global APT activity, AI usage, actor and tactic profiles, and implications Rise in volumes of AI-powered cyberattacks Major cyber events in 2024 Malware and malicious payload trends Cyberattack types and targets Vulnerability exploit attempts on CVEs Attacks on counties – USA Expansion of bot farms – how, where, and why In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East Why are attacks on smart factories rising? Cyber risk predictions Axis of attacks – Europe Systemic attacks in the Middle East Download the full report from here: https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/

UiPath Test Automation using UiPath Test Suite series, part 3

DianaGray10

Recently uploaded (20)