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Professional Development, Training and Education

ISCBintel and Achievements

ISCB Hosts the Second Youth Bioinformatics Symposium


The International Society for Computational Biology (ISCB) in partnership with George Mason University, will host the Youth Bioinformatics Symposium (YBS), Exploring Computational Biology at George Mason University in winter 2019.

At our first YBS, in 2016, nearly 100 students from the greater Washington DC area gathered for this event. This engaging one-day event introduces students to the amazing world of computational biology, allowing them to engage with and learn about three popular tools used in research in our hands-on workshop, inform them of the many career areas that bioinformatics is now appearing in, and spark the spirit of competition in our team-based mini science challenges.

We hope you join us to make YBS 2019 just as successful!

REGISTRATION IS NOW CLOSED



Click here to see the 2016 symposium photos.


What IS computational Biology?! Watch this video to find out and click here for additional resources.

 


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TECHNOLOGY TALKS



Bioinformatics as the main protagonist of the microbiome field

Speaker: Dr. Daniel Almonacid

The human microbiome, the microorganisms that live in and on the human body, is one of the most diverse ecosystems on Earth. Our mission at uBiome is to advance the science of the microbiome and make useful products that improve human life. The company’s technological platform is based on the largest microbial dataset in the world (over 300,000 samples), allowing us unprecedented coverage of the microbial diversity across multiple sites of the human body. Using nucleotide sequencing, including our own approach called Precision Sequencing TM, bioinformatics, and machine learning methods, we are developing precision medicine solutions based on microbiome information, empowering doctors, patients, and citizen scientists to improve their quality of life.

Our current portfolio goes from tools for citizens scientists to study their own microbial communities (Explorer TM), to screening tests that can inform doctors of conditions associated with intestinal health (SmartGut TM) and vaginal health (SmartJane TM). The information generated with these analyses allow us continuous improvement of these products.  Additionally, we continually monitor the scientific literature to add new targets as well as novel correlations in our tests. Moreover, the sequencing information combined with the metadata collected from patients has allowed us to discover novel correlations between the microbiome and host conditions, some of which we have been able to understand mechanistically. This knowledge has presented uBiome with the opportunity to in silico design and test drugs that target the microbiome (drugs for bugs), drugs that are naturally produced by the microbiota to modulate the host (drugs from bugs), in addition to identifying and testing potential live biotherapeutics for different health conditions (bugs as drugs).

In this talk I will provide an overview of the work that we are currently doing at uBiome, emphasizing the use of reproducible approaches (both in the laboratory and bioinformatics).  This talk will also highlight the road that uBiome is taking from the research and implementation of clinical tests, toward the development of therapeutics products, having bioinformatics as the main protagonist.


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SPECIAL SESSIONS



links in this page: Bioinformatics EducationDevelopment and application of tools for microbiome studies | Integrative approaches for RNA biology | Precision Medicine | Workshop on Docker | UCSC Genome Browser Workshop | Higher Understanding with Lower Dimensions


Special Sessions at GLBIO 2019

Many of the sessions listed below will consider submissions for contributed talks, including full papers in addition to our regular track. All such papers should be submitted through EasyChair, by the relevant GLBIO 2019 submission deadline. Please contact the organizer of the individual sessions for more information. 


Bioinformatics Education

Accepting abstracts only for oral presentations through EasyChair.
The GLBIO 2019 Special Session on Bioinformatics Education seeks to create a platform for presentation and discussion on the topic of bioinformatics education broadly defined.  The session will mix invited talks from leaders in bioinformatics education with contributed talks and posters from the community.  The intention is to provide a broad representation of perspectives, goals, and topics engaging the bioinformatics education community.  The session is soliciting short abstracts for proposed talks or posters.  Topics of interest include but are not limited to

  • bioinformatics curriculum development for bioinformatics professionals, life scientists, healthcare professionals, K-12 students, or other communities
  • education policy and practices
  • pedagogical strategies or experiences
  • community education resources
  • outreach and diversity efforts
  • case studies in bioinformatics education


The session will conclude with a Panel Discussion and Community Forum organized around the theme of identifying the aims for Bioinformatics Education community over the next five years.

Organizer(s): This email address is being protected from spambots. You need JavaScript enabled to view it.
Web page: https://qubeshub.org/community/groups/glbioedu

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Development and Application of Tools for Microbiome Studies

Accepting abstracts only for oral presentations through EasyChair.
Microbiome research is a rapidly growing area of science. Over the last decade, the number of microbiome sequencing studies has expanded enormously, exploring the intricate communities of microbes within soil, water, the built environment, and the human body, amongst others. There is a need to ensure that adequate expertise and infrastructure is in place to meet the challenge of analyzing the data generated as well as a robust and reliable framework for interpreting the data. This session will cover (1) different computational and statistical methods for analyzing microbiome data sets, and (2) investigations of microbiomes uncovering new insight into functions and dynamics.

Organizers:This email address is being protected from spambots. You need JavaScript enabled to view it. and This email address is being protected from spambots. You need JavaScript enabled to view it.
Website: https://microbiome.wisc.edu/events/glbio2019/


Integrative approaches for RNA biology

Accepting full papers and abstracts for oral presentations through EasyChair.
Post-transcriptional processes play a key role in eukaryotic gene regulation, yet it is not well understood how such processes contribute to the level of functional RNAs within the cell. Such regulation is orchestrated through a variety of mechanisms acting on all aspects of RNA metabolism, including pre-mRNA splicing, stability, polyadenylation, localization, editing, modification, and translation. The diversity of these mechanisms as well as the the increase in RNA-related high-throughput sequencing approaches highlight the need for research into new computational tools addressing post-transcriptional gene regulation.

This session focuses on research findings and methods related to the sequence and structure of RNA as well as its post-transcriptional gene regulation. These include but are not limited to the analysis of transcriptomics and protein-RNA interaction datasets, novel methods for interpretation of single-cell transcriptomes and approaches for RNA structure prediction. The session comprises of invited and selected talks, as well as a workshop on analyses of RNA splicing from high-throughput transcriptome-wide sequencing, and identification of protein/RNA binding sites from CLIP-seq data. The audience is expected to have a basic understanding and experience with computational biology, but not to be experts on RNA biology or the current computational and experimental approaches used in RNA research.

Organizer(s): This email address is being protected from spambots. You need JavaScript enabled to view it. and This email address is being protected from spambots. You need JavaScript enabled to view it.
Website: http://www.iupui.edu/~jangalab/rss_glbio19/

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Precision Medicine

Accepting abstracts only for oral presentations through EasyChair.
Advances in computing have led to a data-driven revolution in biology and promise to guide progress in precision medicine. This session will explore the spectrum of challenges and opportunities in precision medicine, including genomics, electronic health record analytics, and drug discovery. Confirmed speakers apply systems approaches to disease, biomarker, and other complex trait prediction by building computational models that leverage and integrate similarity in genetic, transcriptomic and other omics-level data. The intended audience for this session includes those interested in integrative genomics, statistical modeling, machine learning, and human population genetics applications in medicine.

Organizers: This email address is being protected from spambots. You need JavaScript enabled to view it., This email address is being protected from spambots. You need JavaScript enabled to view it., and This email address is being protected from spambots. You need JavaScript enabled to view it.
Website: http://glbio19-precisionmedicine.strikingly.com/

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Workshop on Docker

Half-day Tutorial.  Will not accept submissions.
This workshop aims to be the next step in reproducibility for computational biologists and will focus on using and developing software containers. We will review best practices for practicing reproducible research and teach participants how to use Docker, a popular software for containerization (which can also be used by Singularity, another commonly used containerization platform). Using containers can help overcome the many interoperability and dependency issues often encountered when distributing or installing software. Docker images used conjunction with continuous integration is considered to be a possible solution for the reproducibility crisis plaguing research at large. Similar to a Carpentries workshop, a majority of the proposed workshop will be hands-on live-coding. Workshop attendees are expected to have familiarity with the Unix shell and git/github, bring their own laptops, and follow along with the training.

Organizers: This email address is being protected from spambots. You need JavaScript enabled to view it.
Website: https://uw-madison-datascience.github.io/2019-05-19-glbio-docker/

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UCSC Genome Browser Workshop

Half-day Tutorial.  Will not accept submissions.
As the flood of data from high-throughput sequencing threatens to overwhelm scientists with data generated within individual labs and distributed on the web, visualization becomes even more important.  The UCSC Genome Browser has developed tools that assist in understanding the import of data and provides a platform to view data from multiple sources together.  The endpoint of a data pipeline need not be statistical or tabular.  A potent visualization tool such as the Browser can add an important dimension to data analysis.

This UCSC Genome Browser workshop will offer a tour through recent data releases and new features.  New data include a pre-computed CRISPR guides track on human, mouse and other genome assemblies, a mapping of transcript-specific GTEx expression data, a Gene Interactions track which collects data from multiple curated databases and from data-mining of the literature, and gnomAD.  Recently added features include multi-region mode, which allows for display of exons only or of any regions specified by the user, whether contiguous in the genome or not and Track Collections, which allows co-configuration of multiple tracks and new data formats for loading your data (interation and barChart).

Organizers:  This email address is being protected from spambots. You need JavaScript enabled to view it. and This email address is being protected from spambots. You need JavaScript enabled to view it.
Website: https://users.soe.ucsc.edu/~kuhn/workshops/glbio2019/ 

 

Higher Understanding with Lower Dimensions
Tutorial on Dimensionality Reduction Methods for Biomedical Data
Student Run Event

Evening Tutorial.  Will not accept submissions.
Many real-world datasets are high-dimensional in their raw form but have low-dimensional structure, groupings, or representations. Dimensionality reduction methods have been applied to various biomedical datasets with the aim of cancer subtype extraction from mutational signatures, genotype-to-phenotype mapping, gene regulatory program identification, unsupervised multi-omics data integration, and cell differentiation trajectory visualization. This workshop will provide an opportunity to explore a handful of powerful dimensionality reduction methods: matrix factorization, PCA/LDA/GDA, t-SNE and UMAP, diffusion map, and autoencoders. All demos and exercises will use real biomedical datasets from single cell RNA-seq, Hi-C, and de-identified medical records.
 

Organizers: Brittany Baur, Erika Da-Inn Lee, Xiaotong Liu and Henry Neil Ward
Website: https://dimension-reduction.github.io/


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SPONSORS & EXHIBITORS



Gold Sponsors


Bronze Sponsors


Copper Sponsors


General Sponsors


Lunch N' Learn Exhibitors


Exhibitors


Click thumbnail to view pdf of Exhibitors map


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ISCB Town Hall



Topic: ISCB Town Hall
Date: Sunday, July 8 (12:45 PM - 1:45 PM)
Room: Columbus IJ

Description
Join us at the ISCB Town Hall meeting on Sunday, July 8, from 12:45 PM - 1:45 PM to learn more about the latest programs, initiatives, and conferences. This is also your chance to help shape the future of ISCB by providing feedback and suggestions. The Town Hall will close with a celebration of achievement with the announcement of the Student Council Symposium award winners.

TOP 10 PAPERS READING LIST, 2016-2017

Top Reading Papers 2016 - 2017 - RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges



As selected at RECOMB/ISCB Regulatory systems Genomics 2017
(Papers are listed alphabetically by title.  Due to a draw, this year's list contains 11 papers.)

A prior-based integrative framework for functional transcriptional regulatory network inference, Siahpirani A, Roy S. Nucleic Acids Res 45(4):e21

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data, Schep AN, Wu B, Buenrostro JD, Greenleaf WJ. Nat Methods 14(10):975-978

Denoising genome-wide histone ChIP-seq with convolutional neural networks, Koh PW, Pierson E, Kundaje A. Bioinformatics 33(14):i225-i233

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions, Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen T, Kellis M. Nat Biotechnol 34(11):1180-1190

Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility, Lamparter D, Marbach D, Rueedi R, Bergmann S, Kutalik Z. PLoS Comput Biol 13(1):e1005311

Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network, Dhingra P, Martinez-Fundichely A, Berger A, Huang FW, Forbes AN, Liu EM, Liu D, Sboner A, Tamayo P, Rickman DS, Rubin MA, Khurana E. Genome Biol 18:141

Is a super-enhancer greater than the sum of its parts?, Dukler N, Gulko B, Huang YF, Siepel A. Nat Genet 49:2-3

Quantifying the impact of non-coding variants on transcription factor-DNA binding, Zhao J, Li D, Seo J, Allen AS, Gordan R. Res Comput Mol Biol 10229:336-352

Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines, Cao Q, Anyansi C, Hu X, Xu L, Xiong L, Tang W, Mok MTS, Cheng C, Fan X, Gerstein M, Cheng ASL, Yip KY. Nat Genet 49(10):1428-1436

SMiLE-seq identifies binding motifs of single and dimeric transcription factors, Isakova A, Groux R, Imbeault M, Rainer P, Alpern D, Dainese R, Ambrosini G, Trono D, Bucher P, Deplancke B. Nat Methods 14(3):316-322

Transcription factor family-specific DNA shape readout revealed by quantitative specificity models, Yang L, Orenstein Y, Jolma A, Yin Y, Taipale J, Shamir R, Rohs R. Mol Syst Biol 13(2):910

CONGRATULATIONS TO ALL AUTHORS!


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GETTING TO NYC



Links within this page:
Plane | Train | Bus | Car


Whether you live across the Hudson or across the Atlantic, getting to NYC is easy. If you’re coming from outside the United States, check this page for visa information.

See below for the best ways to reach the five boroughs from anywhere in the world.

By plane If you’re coming from far away, you’ll probably want to fly into one of the New York City area’s major airports. There are a number of hotels conveniently located near the City’s airports.


By Plane


Below, you'll find a list of NYC-area airports, along with the best ways to get from those airports to Manhattan. There are more than a hundred air carriers traveling to NYC from all over the country and the world, including American Airlines, Delta, JetBlue and United.

Air travelers to New York City may arrive at John F. Kennedy International Airport (JFK) or LaGuardia Airport (LGA), both in Queens, or Newark Liberty International Airport (EWR) in neighboring New Jersey. LaGuardia primarily serves domestic destinations, and also offers flights to select Canadian and Caribbean destinations. Kennedy and Newark both serve domestic and international destinations. Visitors can reach Manhattan from all three airports by using taxis, buses, subways and/or commuter trains. Other metropolitan-area airports include Stewart International Airport (SWF), Westchester County Airport (HPN) and MacArthur Airport (ISP). For those interested, there are a number of hotels conveniently located near the City's airports.

John F. Kennedy International Airport (JFK)
Jamaica, Queens, NY 11430
718-244-4444

New York's largest airport serves more than 80 airlines, most of which are international. It is approximately 15 miles from Midtown Manhattan. Here's how to get to Midtown Manhattan from JFK:

  • Taxi: $52.50 flat fare (non-metered), plus bridge and tunnel tolls and gratuity; 30 to 60 minutes to Midtown Manhattan, depending on traffic and road conditions. For more information, call 212-NYC-TAXI or visit the Taxi and Limousine Commission website.
  • AirTrain JFK: $5 (children under 5 are free); AirTrain links the airport to the subway and Long Island Rail Road. AirTrain also offers free service between points in the airport.
  • Subway: one ride (in addition to AirTrain fare) from the A subway stop at the Howard Beach/JFK Airport station or the E, J or Z subway stop at the Sutphin Blvd./Archer Ave./JFK Airport station; 60 to 75 minutes to Midtown Manhattan.
  • Long Island Rail Road (LIRR): $7.25–$10 (children under 5 are free), depending on time of day (in addition to AirTrain fare) for the trip between LIRR's Jamaica Station and Penn Station; on Saturday and Sunday, the fare is $4.25. The trip is 20 minutes to Midtown Manhattan (not including AirTrain ride).
  • City bus: For details, visit tripplanner.mta.info.
  • Shuttle bus: NYC Airporter, Go Airlink NYC and SuperShuttle.
  • Private car service: See this list of providers.
  • Car rental: Companies at JFK include Avis, Budget, Dollar, Enterprise, Hertz and National.


LaGuardia Airport (LGA)
Jackson Heights, Queens, NY 11371
718-533-3400

This is New York's second-largest airport, with nearly 20 airlines serving mostly domestic destinations, as well as Canada and the Caribbean, from four passenger terminals. LaGuardia is on the northern shore of Queens, directly across the East River (about 8 miles from Midtown Manhattan). Here's how to get to Midtown Manhattan from LaGuardia:


Newark Liberty International Airport (EWR)
Newark, NJ 07114
973-961-6000

Newark Airport, with more than 30 airlines (many of which are international), is across the Hudson River from New York City—16 miles from Midtown Manhattan. Here's how to get to Midtown Manhattan from Newark Liberty:

  • Taxi: Traveling to Manhattan, metered fare; approximately $50 to $75, plus bridge and tunnel tolls and gratuity; 45 to 60 minutes to Midtown Manhattan. During weekday rush hours (6–9am and 4–7pm) and on weekends (Saturday–Sunday, noon–8pm), there is a $5 surcharge for travel to anywhere in New York State except Staten Island. When traveling to the airport from Midtown Manhattan, service is via New York City’s regulated yellow taxis. Metered fares range $69–$75, plus a $17.50 surcharge in addition to tolls and gratuity.
  • AirTrain Newark: Costs vary by destination. AirTrain links to the airport via NJ Transit and Amtrak's Newark (or EWR) train station; 45 to 90 minutes to Midtown Manhattan, requiring a transfer from the AirTrain line to the NJ Transit line (be sure to keep your ticket after using it to exit the AirTrain station, as it is also used for the NJ Transit fare) or Amtrak. AirTrain also offers free service between points in within the airport complex, including hotels and parking. Look for signs marked “Monorail/AirTrain Link” (do not follow signs for Ground Transportation).
  • Shuttle bus: NYC Airporter, Go Airlink NYC, Olympia Airport Express and SuperShuttle.
  • Private car and limousine service: Dial 7, Carmel and Uber.
  • Car rental: Companies at Newark include Avis, Budget, Dollar, Enterprise, Hertz and National.


Stewart International Airport (SWF)
New Windsor, NY 12553
845-838-8200

Stewart International Airport is 60 miles north of New York City. Here's how to get to Midtown Manhattan from Stewart:

  • Bus/train: Leprechaun Lines runs a $1 shuttle bus on their Newburgh-Beacon-Stewart commuter line, which connects to the Beacon train station. There, use Metro-North Railroad for direct service to Grand Central Terminal ($16 off-peak, $21.25 peak); 70 to 90 minutes to Midtown Manhattan.


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By Train


New York City has two main rail stations in Midtown: Grand Central Terminal (on the east side) and Penn Station (on the west side). Each is also served by numerous bus and subway lines. Grand Central is served by Metro-North Railroad, which goes to NYC suburbs in New York and Connecticut. Penn Station is served by the following: Long Island Rail Road, a commuter railroad serving Long Island; Amtrak, the US national passenger railroad, serving many points throughout the country; and NJ Transit, a commuter line serving points in New Jersey.

  • Rail Terminals
    • Grand Central Terminal
      Park Avenue and East 42nd Street (between Lexington and Vanderbilt Avenues)
      212-532-4900
      Grand Central is the main terminal for Metro-North Railroad services. Subway lines here include the 4, 5, 6, 7 and S (shuttle between Grand Central and Times Square). For MTA bus details, visit tripplanner.mta.info.

      Aside from being a transit hub, Grand Central is also a landmark and an attraction unto itself. The Main Concourse boasts an immense 88,000 square feet of space, and on sunny days is bathed in light from its giant arching windows. Grand Central's 12-story ceiling is painted with stars and gilded zodiac constellations. Not only might Grand Central be the globe's most beautiful train station, the 49-acre terminal is also one of the world's largest. There are numerous shops of all varieties here, including an Apple Store, MAC Cosmetics and Tumi. The dining concourse on the lower level features a wide selection of eateries, and in Grand Central Market, fresh and prepared foods—ranging from baked goods to gourmet teas—are available.
    • Penn Station
      Seventh to Eighth Avenues, between West 31st and West 33rd Streets
      Penn Station is the main terminal for Long Island Rail Road, and a terminal for Amtrak and NJ Transit. Subway lines here include the 1, 2, 3, A, C and E. For MTA bus details, visit tripplanner.mta.info.

      Penn Station's main concourse features information booths, restaurants, waiting rooms and public restrooms to accommodate the thousands of passengers who pass through the terminal each day. In 2016, the new West End Concourse will open providing additional access to the station from 8th avenue. Car rental offices are nearby.
  • Rail Services
    • Amtrak
      800-872-7245, 212-630-6400
      Amtrak is the national passenger railroad of the United States. New York City's Penn Station is their busiest station in the nation, serving hundreds of thousands of passengers each year. The company offers numerous packages and deals, including special passes allowing international visitors to make multiple stops throughout the country.
    • Long Island Rail Road (LIRR)
      718-217-5477
      This commuter railroad operates out of Penn Station and serves 124 stations in Nassau County, Suffolk County, Queens, Brooklyn and Manhattan, transporting some 81 million customers each year. Destinations include the Belmont Park racetrack, Citi Field, Jones Beach, the Hamptons and Montauk.
    • Metro-North Railroad
      212-532-4900, 877-690-5114
      The second-largest commuter train line in the United States, Metro-North operates out of Grand Central Terminal. The historic roots of the operation go back to 1832, when the enterprise was known as the New York & Harlem Railroad, a horsecar line in Lower Manhattan. Today, with 775 miles of track, Metro-North goes to 121 stations (in seven New York State counties—Dutchess, Putnam, Westchester, Rockland, Orange, Bronx and New York (Manhattan)—and Connecticut's New Haven and Fairfield counties).
    • NJ Transit
      973-275-5555, TTY 800-772-2287
      This rail system features 12 lines in three divisions (Hoboken, Newark and the Atlantic City Rail Line) with frequent service throughout New Jersey (Atlantic City and the Jersey Shore are popular stops) and New York (Rockland and Orange counties)—and, of course, into and out of New York City via Penn Station. For schedules and fares, visit the NJ Transit website.
    • PATH (Port Authority Trans Hudson)
      800-234-PATH
      The PATH provides rapid transit between several stops in New York City, along with locations in Newark, Harrison, Jersey City and Hoboken in New Jersey. Air travelers can connect to the PATH from Newark Liberty International Airport. The service operates from the Penn Station in Newark (not the same as Manhattan's Penn Station) to Lower and Midtown Manhattan. The PATH's 33rd Street station (on Sixth Avenue, in Herald Square) in Manhattan is one avenue from Amtrak, Long Island Rail Road and NJ Transit trains at Penn Station.


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By Bus


There are a number of affordable, convenient bus lines that travel to New York City from around the United States and parts of Canada. These include BoltBus, Megabus and Greyhound.

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By Car


Use Google Maps for driving directions to New York City. Also, make sure you know where to park: you may want to use an app like SpotHero to find and compare parking spots and locations.

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RSG and DREAM General Questions

Bel Hanson, Conference Manager
Tel: 1-571-293-0286

Source: NYC The Official Guide


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Exclusively for members

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