BEGIN:VCALENDAR
CALNAME:Nextflow Summit 2024 - Boston
NAME:Nextflow Summit 2024 - Boston
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VERSION:2.0
X-WR-CALNAME:Nextflow Summit 2024 - Boston
BEGIN:VTIMEZONE
TZID:Eastern Standard Time
X-LIC-LOCATION:America/New_York
BEGIN:STANDARD
DTSTART:20241103T020000
RRULE:FREQ=YEARLY;BYDAY=1SU;BYMONTH=11
TZNAME:EST
TZOFFSETFROM:-0400
TZOFFSETTO:-0500
END:STANDARD
BEGIN:DAYLIGHT
DTSTART:20250309T020000
RRULE:FREQ=YEARLY;BYDAY=2SU;BYMONTH=3
TZNAME:EDT
TZOFFSETFROM:-0500
TZOFFSETTO:-0400
END:DAYLIGHT
END:VTIMEZONE
BEGIN:VEVENT
DESCRIPTION:Registration\, coffee\, and pastries.
DTEND:20240521T100000
DTSTAMP:20260413T034932Z
DTSTART:20240521T090000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Registration and pastries
UID:SZSESSION5870a391-4b49-4373-bcc7-56673c7cf5f9
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:A short welcome to the nf-core hackathon.
DTEND:20240521T103000
DTSTAMP:20260413T034932Z
DTSTART:20240521T100000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Hackathon welcome
UID:SZSESSIONfc2b00e0-b68f-4fe9-85f1-48c52c91a932
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:A short welcome to the Nextflow training.
DTEND:20240521T103000
DTSTAMP:20260413T034932Z
DTSTART:20240521T100000
LOCATION:Training
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Training welcome
UID:SZSESSION0c7d3f47-6419-4394-ad72-fc6f1bc37138
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Hackathon: Session 1
DTEND:20240521T130000
DTSTAMP:20260413T034932Z
DTSTART:20240521T103000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Hackathon: Session 1
UID:SZSESSIONd76e351e-2e0f-4636-ac4e-cf441737c975
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Training: Session 1
DTEND:20240521T130000
DTSTAMP:20260413T034932Z
DTSTART:20240521T103000
LOCATION:Training
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Training: Session 1
UID:SZSESSION6cb0159b-dd83-4801-8e1d-fe013e9802a5
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:
DTEND:20240521T140000
DTSTAMP:20260413T034932Z
DTSTART:20240521T130000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Lunch
UID:SZSESSION2ac879b0-1340-4676-8bd7-e5a7f9853e13
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Hackathon: Session 2
DTEND:20240521T164500
DTSTAMP:20260413T034932Z
DTSTART:20240521T140000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Hackathon: Session 2
UID:SZSESSIONc3103c79-1d49-44ae-9f84-d9ed960ed1c4
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Training: Session 2
DTEND:20240521T164500
DTSTAMP:20260413T034932Z
DTSTART:20240521T140000
LOCATION:Training
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Training: Session 2
UID:SZSESSION419c9f05-cc4c-4148-aedb-94f2daedbdae
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Hackathon daily 1 sync
DTEND:20240521T172000
DTSTAMP:20260413T034932Z
DTSTART:20240521T164500
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Hackathon daily 1 sync
UID:SZSESSIONe1f8b17c-2d8c-499c-9e05-fd74491a9d41
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Training day 1 review
DTEND:20240521T172000
DTSTAMP:20260413T034932Z
DTSTART:20240521T164500
LOCATION:Training
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Training day 1 review
UID:SZSESSIONeb4e30c0-4302-4494-a683-353bf98f0bcc
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Join us for an evening of tech-infused mini golf\, networking\
 , food and drinks at Puttschack! \n\nConnect with fellow participants of 
 the Nextflow nf-core hackathon and training while enjoying a relaxed and 
 entertaining atmosphere in the vibrant Seaport area of Boston. \n\nCompli
 mentary food and drinks will be provided. \n\nAddress: 58 Pier 4 Blvd.\, 
 Boston\, MA 02210
DTEND:20240521T210000
DTSTAMP:20260413T034932Z
DTSTART:20240521T180000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Hackathon & training social event
UID:SZSESSION43538679-239c-4509-87f8-fdbcaa65d4fb
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Arrivals and pastries
DTEND:20240522T100000
DTSTAMP:20260413T034932Z
DTSTART:20240522T090000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Arrivals and pastries
UID:SZSESSION36dd0092-9b28-4ad6-8d4b-0d41e1ce6b16
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Hackathon: Session 3
DTEND:20240522T130000
DTSTAMP:20260413T034932Z
DTSTART:20240522T100000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Hackathon: Session 3
UID:SZSESSION10ea3714-c6af-4274-82f3-9e71a1aa458c
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Training: Session 3
DTEND:20240522T130000
DTSTAMP:20260413T034932Z
DTSTART:20240522T100000
LOCATION:Training
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Training: Session 3
UID:SZSESSIONa9c25a02-47b9-4529-8743-3b32e8f731ba
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Lunch
DTEND:20240522T140000
DTSTAMP:20260413T034932Z
DTSTART:20240522T130000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Lunch
UID:SZSESSIONaf2dd085-f7a7-46b7-87e1-f1047b171207
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Hackathon: Session 4
DTEND:20240522T164500
DTSTAMP:20260413T034932Z
DTSTART:20240522T140000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Hackathon: Session 4
UID:SZSESSIONf7bb0b45-c44f-4e9a-ab9c-c7823a8b0901
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Training: Session 4
DTEND:20240522T164500
DTSTAMP:20260413T034932Z
DTSTART:20240522T140000
LOCATION:Training
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Training: Session 4
UID:SZSESSION1c77da5c-98ad-4400-86cd-a4f5a3d6db0e
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:
DTEND:20240522T171500
DTSTAMP:20260413T034932Z
DTSTART:20240522T164500
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Hackathon wrap-up
UID:SZSESSIONacccb952-6a76-49bc-ac06-72097f46de27
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Training day 2 review
DTEND:20240522T171500
DTSTAMP:20260413T034932Z
DTSTART:20240522T164500
LOCATION:Training
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Training day 2 review
UID:SZSESSION32cfc05d-5f04-422f-91f4-a87d3a7aaf13
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Registration\, coffee\, and pastries.
DTEND:20240523T093000
DTSTAMP:20260413T034932Z
DTSTART:20240523T083000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Registrations and pastries
UID:SZSESSIONbdb7c039-2666-40de-98b5-457e3c23c710
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Evan Floden
DTEND:20240523T094500
DTSTAMP:20260413T034932Z
DTSTART:20240523T093000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Summit welcome
UID:SZSESSION658545
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Jason Niehaus\n\nPlasmids are ubiquitous tools found 
 in molecular biology laboratories around the world\, where they serve a v
 ariety of uses such as transferring DNA sequences into a target cell\, mo
 difying gene expression\, or monitoring biological pathways and component
 s. Addgene was founded as a nonprofit repository for DNA-based biological
  reagents\, such as plasmids\, in order to accelerate scientific research
  by improving access to high-quality research materials. Our quality cont
 rol process has evolved over time to keep pace with DNA sequencing techno
 logies where we now fully sequence every plasmid deposited with us. In or
 der for our quality control team to analyze more than 1000 sequences each
  month\, we needed to automate our existing bioinformatics scripts and ce
 ntralize a standardized workflow.\n\nUsing Nextflow\, we created a workfl
 ow for processing an entire sequencing run from an Illumina MiSeq instrum
 ent. The raw sequencing data is retrieved\, converted to FASTQ\, cleaned 
 with various programs from the BBTools suite\, and assembled into complet
 e\, circularized sequences using open-source sequence assembly tools such
  as SPAdes and Shovill. We deployed our workflow in Seqera Platform so th
 at anyone on our quality control team could launch the workflow\, without
  needing to use a command line interface. Additionally\, we reduced our c
 ompute costs by provisioning the required resources as needed\, while all
 owing for easy scaling should our intake or turn-around time requirements
  change.\n\nWith the success of our first workflow in Seqera Platform\, w
 e are looking to add new modules to further automate sequence analysis by
  screening for contaminant sequences in the FASTQ sequence reads and prov
 ide a quality assessment of the final assembled sequence.
DTEND:20240523T100000
DTSTAMP:20260413T034932Z
DTSTART:20240523T094500
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Constructing a quality control platform for plasmid verification
UID:SZSESSION640275
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Seamus Mawe\n\nBiomedical imaging presents a case whe
 re not only analyses become very slow as the number of images increases b
 ut can also preclude the use of more traditional acceleration options suc
 h as GPUs due to the large memory footprint of individual data points (gi
 gapixel images). However\, NextFlow significantly and easily improves the
  scalability of analyses that can be split into many independent parts\, 
 such as individual images from a large image set. Using NextFlow\, we hav
 e created reusable and portable analysis pipelines that can effectively a
 dapt to both available resources and the computational needs of various d
 atasets. In this talk\, I will cover our use of NextFlow in the analysis 
 of a 8.1TB dataset of whole-slide images\, discussing both the substantia
 l gains from NextFlow-enabled parallelization and some of the pitfalls fo
 r our large-format images\, including getting the auto submission of jobs
  to work with our Slurm setup and some of the issues we had with our inte
 rmediary files.
DTEND:20240523T101500
DTSTAMP:20260413T034932Z
DTSTART:20240523T100000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Parallelization of computer vision over large corpora of gigapixel
  biomedical images
UID:SZSESSION641714
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Jason Fan\n\nGroovy is the underlying programming lan
 guage for Nextflow and can be used to model input metadata such as sample
  sheets.  Through defining Groovy classes in the library directory\, Next
 flow is able to utilize these data classes to store both source and deriv
 ed metadata\, for example Sample Sheets\, Reference data\, and more.  In 
 contrast to tuples and ad-hoc inline comments\, Groovy classes when used 
 within Nextflow workflows provide a complied\, typed\, and concise specif
 ication of metadata and object models allowing for safer and easier-to-re
 ason workflows.
DTEND:20240523T103000
DTSTAMP:20260413T034932Z
DTSTART:20240523T101500
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Get into the Groovy: using Groovy to model sample sheets\, input a
 nd metadata\, and more
UID:SZSESSION649698
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Geraldine Van der Auwera\n\nThe Nextflow and nf-core 
 communities continue to thrive and are growing at a phenomenal rate. As w
 e approach new milestones\, Geraldine will review some of the major proje
 cts and initiatives that have taken place during the past 6 months and lo
 ok ahead to the new projects on the horizon.
DTEND:20240523T110000
DTSTAMP:20260413T034932Z
DTSTART:20240523T103000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Community updates
UID:SZSESSION656894
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Coffee and pastries
DTEND:20240523T113000
DTSTAMP:20260413T034932Z
DTSTART:20240523T110000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Coffee break
UID:SZSESSIONe1681e85-da42-404d-8792-cd939e3a5cc0
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Andres Fernandez Benevento\n\nZS Discovery\, part of 
 ZS Associates’ R&D practice area\, partners with pharmaceutical and biote
 chnology companies to tackle challenging scientific and technological asp
 ects of the Research & Development lifecycle. In the era of multiomic dat
 asets and big data\, building and deploying automated\, robust workflows 
 is critically important for increasing reproducibility and decreasing the
  time for achieving actionable results. Here\, we will present a summary 
 of our experience developing customized pipelines\, modules and infrastru
 cture\, and how we contributed learnings from our work towards the develo
 pment of open-source pipelines hosted on nf-core. Our experiences and lea
 rnings can be used as the basis of a framework for developing similar wor
 kflows\, building on insights gained to avoid pitfalls and deliver rapid 
 scientific impact.
DTEND:20240523T114500
DTSTAMP:20260413T034932Z
DTSTART:20240523T113000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Innovation through Collaboration: Developing bioinformatic pipelin
 es and sharing with nf-core
UID:SZSESSION667383
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Brenna Novotny\n\nThe rapidly growing field of spatia
 l biology allows unprecedented insight into the arrangement and interacti
 ons of cells as they occur in our bodies. Understanding single-cell-level
  spatial relationships can help us answer important clinical and biologic
 al questions. How do individual immune cells infiltrate and fight tumors 
 in cancer patients? How does the arrangement of neurons affect our brains
 ’ functioning as we age?\n\nSingle cell multiplexed protein imaging captu
 res protein abundances on a cellular level and is one type of spatial omi
 cs data (high-resolution data measurements for spatial biology studies). 
 Multiplexing allows measurement of multiple proteins on the same tissue s
 ection\, facilitating detailed insight into cell-cell interactions and fu
 nctional states in healthy or diseased tissue. Cell phenotyping is a vita
 l step in the analysis of these data because downstream spatial analysis 
 depends on a complete understanding of the cell types present in the tiss
 ue. Many techniques for cell phenotyping have been developed\, including 
 unsupervised clustering\, linear modeling\, and supervised classification
 . Supervised techniques\, while accurate\, can be very time-consuming for
  subject matter experts\, requiring hours of work to annotate a represent
 ative sample of cells. Unsupervised clustering allows researchers to quic
 kly evaluate the presence of cell types based on expected protein signatu
 res. Implementing these methods efficiently can accelerate the phenotypin
 g process by providing a jumping-off point for further iterations.\n\nWe 
 have developed SpaFlow\, a Nextflow pipeline which runs quality control c
 hecks and three unsupervised cell phenotyping methods. Implementing the w
 orkflow as a Nextflow pipeline allows us to greatly reduce time and effor
 t versus setting up custom R and Python scripts\, leading to a shorter tu
 rnaround time and more cost-effective analysis for investigators. To date
 \, we have processed batches of up to 300 images and 850\,000 cells in un
 der 30 minutes\, saving hours and in some cases days of manual processing
 . This talk will describe our Nextflow pipeline and the value it brings t
 o our work\, as well as our experience learning and developing Nextflow a
 s first-time users.\n
DTEND:20240523T120000
DTSTAMP:20260413T034932Z
DTSTART:20240523T114500
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:SpaFlow: A Nextflow pipeline for single cell phenotyping in spatia
 l omics
UID:SZSESSION641330
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Alex Valcourt Caron\n\nIn the community of diffusion 
 MRI (dMRI)\, laboratories have been processing their data using mostly ol
 d school techniques to do task scheduling\; most of them still process se
 quentially using bash scripts. In our lab\, we started using Nextflow DSL
 1 a few years back to accelerate our processing efficiency\, with moderat
 e success and great feedback from our collaborators and researchers all a
 round the world.\n\nAs our collection of pipelines and users grows - and 
 slowly becomes unmanageable - it is time to actualize once again our soft
 ware ecosystem. This time\, we want to do it so people can follow our lea
 d and take the steps required to accelerate the field of dMRI into the ne
 xt era. Using Nextflow DSL2 and the nf-core suite of tools and standards 
 developed by the community\, we created nf-scil\, a repository of curated
  modules for dMRI processing. We loaded it with a varied collection of pr
 ocesses we love and use daily to process our data\, as well as workflows 
 mimicking common tasks taken on them. Since nf-scil adheres to the core s
 tandards of nf-core\, all modules it proposes get linted\, tested and int
 egrated practically for free\, albeit the user needs to define test cases
 \; they are thus safer to implement in fully-fledged pipelines than their
  DSL1 counterparts.\n\nTo prove the usability of nf-scil\, we used its co
 mponents to port one of our most popular pipelines\, Tractoflow\, into DL
 S2. While its new implementation does not diverge from the previous one i
 n terms of outputs\, Tractoflow is now fully validated\, delivered throug
 h CI/CD and its API auto-generated. This has the potential to save an inc
 redible amount of time to our developers and users\, which can now implem
 ent new modules and pipelines in a continuously integrated and delivered 
 environment. In addition\, it will facilitate making the field of diffusi
 on MRI research more reproducible and its solutions more efficient\, pavi
 ng the way for faster translation to clinical studies of research finding
 s and better usage of computational resources in medical imaging analysis
 .
DTEND:20240523T121500
DTSTAMP:20260413T034932Z
DTSTART:20240523T120000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Mining diamonds with wooden hammers : getting diffusion MRI proces
 sing into the age of steel
UID:SZSESSION641597
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Evan Floden\n\nModern bioinformatics is a collective 
 effort. Today\, the most successful researchers use open source tools and
  approaches from software development\, and leverage the wisdom of the co
 mmunity to advance research and discovery. Our mission at Seqera is to su
 pport this ecosystem by equipping bioinformaticians with the tools they n
 eed to create scalable\, reproducible\, and adaptable solutions\, all gro
 unded in the principles of open science.\n\nContainerized workflow engine
 s like Nextflow have revolutionized the landscape of research and develop
 ment in biopharma\, driving unprecedented efficiencies and output. Howeve
 r\, our vision extends far beyond workflows. We recognize the importance 
 of effective data management\, streamlined analysis\, and seamless transi
 tion from observations to insights. \n\nWe’re also looking forward to unv
 eiling new tools and infrastructure designed to simplify the discovery of
  relevant tools and data\, empowering scientists to navigate the vast lan
 dscape of biotech resources with ease. Additionally\, we're introducing n
 ew capabilities for interactive data analysis within your favorite data s
 cience applications\, bridging the gap between computational tools and us
 er-friendly interfaces. And to further enhance accessibility and flexibil
 ity\, we're providing more convenient access to compute environments and 
 resources\, ensuring that computational power is always within reach.\n\n
 Join us as we embark on this journey to empower scientists with modern so
 ftware development tools\, ushering in a new era of collaboration\, innov
 ation\, and discovery in science.
DTEND:20240523T130000
DTSTAMP:20260413T034932Z
DTSTART:20240523T121500
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Making scientific software accessible to all
UID:SZSESSION657078
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:
DTEND:20240523T140000
DTSTAMP:20260413T034932Z
DTSTART:20240523T130000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Lunch
UID:SZSESSIONce39b407-e0c0-4cef-839c-1e6983a9fa9d
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Sateesh Peri\n\nThe "Cloud Empowerment: Unleashing th
 e Potential of Memory Machine Cloud Snapshot Engine" presentation introdu
 ces an innovative checkpoint solution designed for cloud applications. Th
 e Memory Machine snapshot engine captures the complete application state\
 , including memory and file system\, without requiring any changes to the
  application itself. This technology not only minimizes operational overh
 ead but also automates integration within a customer's job orchestration 
 environment. By facilitating application migration across compute nodes a
 nd execution times\, it significantly reduces operational costs\, acceler
 ates the achievement of results\, and enhances resource utilization. This
  solution presents a transformative approach to managing cloud applicatio
 ns\, offering substantial efficiency and cost benefits.
DTEND:20240523T141500
DTSTAMP:20260413T034932Z
DTSTART:20240523T140000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Cloud Empowerment: Unleashing the Potential of Memory Machine Clou
 d Snapshot Engine
UID:SZSESSION667861
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Lorena Pantano\n\nThe Harvard Chan Bioinformatics Cor
 e is dedicated to fostering collaboration within the Life Sciences\, aimi
 ng to expedite research endeavors using innovative and proven methodologi
 es for high-throughput sequencing data. In 2011\, in response to the abse
 nce of a globally adaptable workflow manager at the time\, Brad Chapman b
 egan developing Bcbio\, a Python-based NGS workflow manager\, for the Cor
 e. Bcbio\, which synthesizes insights learned from numerous projects to p
 rovide best-practice workflows\, gained traction within and beyond the Co
 re and has been embraced by academic researchers\, hospitals\, and indust
 ry alike. Continuously adapting to meet the evolving demands of diverse i
 nfrastructure architectures\, Bcbio has faced the ongoing challenge of re
 maining current and adaptable. Over the past five years\, the nf-core com
 munity has harnessed the capabilities of Nextflow as a workflow manager\,
  fostering the creation of an international\, open-source ecosystem suppo
 rting over 50 pipelines. As ambassadors of analysis reproducibility and s
 calability\, the Harvard Chan Bioinformatics Core recognizes the imperati
 ve of transitioning to nf-core\, albeit a complex process in our organiza
 tion. In this presentation\, we outline the rationale behind this migrati
 on\, elucidate the challenges we are encountering\, and delineate our roa
 dmap toward community-wide adoption\, drawing upon our experiences with t
 he Bcbio platform.
DTEND:20240523T143000
DTSTAMP:20260413T034932Z
DTSTART:20240523T141500
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Perspective: Transitioning through the nf-core era at the Harvard 
 Chan Bioinformatics Core
UID:SZSESSION654779
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Jonathon Keeney\n\nBioCompute is a descriptive standa
 rd (officially "IEEE 2791-2020") that is complimentary to Nextflow\, and 
 a BCO (BioCompute Object) is an instance of a workflow that conforms to t
 he standard. The standard was developed with the input of many  groups fr
 om academia\, private industry\, and government institutions\, most notab
 le the US FDA\, who has officially adopted the standard for describing bi
 oinformatics pipelines used in regulatory submissions\, and who has conti
 nued to invest in the project. This talk will introduce attendees to the 
 project\, and describe recent work that enables the Nextflow engine to ge
 nerate a BCO.
DTEND:20240523T144500
DTSTAMP:20260413T034932Z
DTSTART:20240523T143000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Introduction to BioCompute and Integration with Nextflow
UID:SZSESSION654709
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Paolo Di Tommaso\n\nNextflow\, Wave and Fusion are re
 volutionizing data analysis workflows. In this talk\, we'll cover recent 
 improvements to the core tooling that sits at the heart of Seqera. Learn 
 how we're helping Nextflow to scale to millions of jobs\, with new and im
 prove syntax constructs for building your pipelines. Hear about how Wave 
 is bringing containers in a secure\, extendable and above all user-friend
 ly way to thousands of bioinformaticians across multiple software environ
 ment setups. Finally\, hear how we are capitalising on the initial succes
 s of Fusion and bringing the results we've seen on AWS to other cloud pro
 viders.
DTEND:20240523T153000
DTSTAMP:20260413T034932Z
DTSTART:20240523T144500
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:What’s new in the Nextflow ecosystem
UID:SZSESSION657858
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Coffee and pastries.
DTEND:20240523T160000
DTSTAMP:20260413T034932Z
DTSTART:20240523T153000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Coffee break
UID:SZSESSION5ccff18f-b059-45f5-8646-f4420f922deb
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Alvaro Martinez Barrio\n\nMolecular Pixelation (MPX) 
 is a technology that facilitates the study of relative location of protei
 ns on the cell surface of single cells by NGS readout.  During our talk w
 e will introduce how this is possible using MPX and Pixelator\, our dedic
 ated software which we have developed within Pixelgen Technologies to gen
 erate data for protein abundance\, spatial polarizaty and colocalization 
 of proteins.  We will also demonstrate how we use our Nextflow pipeline\,
  nf-core/pixelator\, to orchestrate data processing for customers and our
  internal R&D team.\n\nIn our publication\, we demonstrate how DNA-oligo 
 tagged antibodies coupled to DNA-pixels are used to assess proteins on th
 e cell surface. We determine the relative location of these proteins by c
 reating neighborhoods that are uniquely identifiable and interconnecting 
 them in a two-step workflow. Based on the information readout\, we build 
 an in-silico graph that allows us to get information about abundance and 
 relative location of constellations of proteins for 1000 cells simultaneo
 usly.\n\nPixelator is a software that transforms raw sequencing data into
  ready-for-analysis PXL files that can be analyzed with our data science 
 tools in R and Python. To our knowledge\, we are the first company to ope
 n-source our pipeline as part of the nf-core initiative and in this talk\
 , we will try to demonstrate how this has benefited our customers and our
  core innovation engine.
DTEND:20240523T161500
DTSTAMP:20260413T034932Z
DTSTART:20240523T160000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Nextflow allows Pixelgen innovation engine to reach the market qui
 cker
UID:SZSESSION667374
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Vlad Savelyev\n\nRebuilding MultiQC for the future: r
 efactoring for interactive use\, new plot types enabled by Plotly\, and s
 caling for large datasets.
DTEND:20240523T163000
DTSTAMP:20260413T034932Z
DTSTART:20240523T161500
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:MultiQC: meet Plotly and notebooks
UID:SZSESSION662754
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Jeffrey Zhou\n\nMany of the principles of nextflow su
 ch as separation of execution environment and code\, the dataflow paradig
 m\, and its ability to work with multiple tools are relatively new to fie
 lds that are used to submitting a few  tightly coupled HPC jobs in an on-
 premise cluster using a job scheduler. However\, with an increased emphas
 is on using cloud computing\, specialized GPU architectures and experimen
 tation with novel AI/ML tooling\, researchers benefit from moving beyond 
 a nest of scripts to a powerful workflow orchestration tool. \n\nIn this 
 talk we demonstrate the problems we are able to solve using Nextflow to p
 rovide "computational pipeline" capabilities in a multi-cloud HPC environ
 ment. Example application areas include sequences of tightly coupled HPC 
 jobs in areas such as automotive engineering\, molecular dynamics\, and m
 aterials science.
DTEND:20240523T164500
DTSTAMP:20260413T034932Z
DTSTART:20240523T163000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Using Nextflow to Orchestrate Tightly-coupled HPC Workloads on Res
 cale
UID:SZSESSION658260
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Corrie Painter\n\nDespite rare cancers accounting for
  25% of adult tumors\, they are difficult to study due to the low disease
  incidence and geographically dispersed patient populations\, which has r
 esulted in significant unmet clinical needs for patients with rare cancer
 s.\n\nThe Broad Institute of MIT and Harvard launched a series of genomic
 s initiative the leveraged partnerships directly with patients to generat
 e and open-source clinic-genomics data at scale\, called Count Me In (CMI
 ).\n\nWe assessed whether this patient-partnered research approach using 
 online engagement can overcome these challenges\, focusing on angiosarcom
 a\, a sarcoma with an annual incidence of 300 cases in the United States.
  We describe the development of the Angiosarcoma Project (ASCproject)\, a
 n initiative enabling US and Canadian patients to remotely share their cl
 inical information and biospecimens for research.\n\nThis patient-partner
 ed approach has catalyzed an opportunity to discover the etiology and pot
 ential therapies for patients with angiosarcoma. Collectively\, this proo
 f-of-concept study demonstrates that empowering patients to directly part
 icipate in research can overcome barriers in rare diseases and can enable
  discoveries.
DTEND:20240523T173000
DTSTAMP:20260413T034932Z
DTSTART:20240523T164500
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY: Breaking Bad Barriers: Overcoming challenges in Rare Cancer Resea
 rch and Innovation
UID:SZSESSION657922
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Drinks and appertizers
DTEND:20240523T200000
DTSTAMP:20260413T034932Z
DTSTART:20240523T173000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Reception
UID:SZSESSION2c5cb8d0-a8e0-47fe-b635-997b43272fed
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Kickstart your second day with a burst of energy and fresh air
 ! \n\nThis will be our second annual Boston Nextflow Summit Sunrise Fun R
 un & Walk - catering to all fitness levels. Whether you’re a seasoned mar
 athoner or someone who just enjoys a leisurely walk\, this activity is de
 signed for everyone.\n\nA professional instructor will guide us through a
  series of warm-ups and stretches\, before and after we hit the route\, a
 long part of the Boston Seaport area\, and will also share tips and help 
 with technique during the run. Not only is this a fantastic opportunity t
 o invigorate your body before the Summit sessions kick in for the day\, b
 ut it’s also a perfect chance to mingle and experience the beautiful morn
 ing scenery together.\n\nFor those who wish to walk instead\, we'll follo
 w a 1.7 mile route which will include a stop at local favorite Tatte Bake
 ry and Cafe.\n\nJoin us for this refreshing morning venture. Lace-up your
  sneakers\, soak in the ambiance\, and let’s start the day on the right f
 oot! 🌟👟
DTEND:20240524T080000
DTSTAMP:20260413T034932Z
DTSTART:20240524T070000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Morning run/walk
UID:SZSESSIONc4bf1397-e1a9-410f-8bd5-70dca01cf44f
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Coffee and breakfast
DTEND:20240524T093000
DTSTAMP:20260413T034932Z
DTSTART:20240524T083000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Arrivals and breakfast
UID:SZSESSION94ca063c-41f1-4f97-8093-be4c8e4dc9d4
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Colby T. Ford\n\nWorkflow tools like Nextflow allow u
 s to standardize and automate our bioinformatics pipelines. Coupled with 
 Docker and Kubernetes\, our pipelines then become portable and scalable. 
 In this session\, we will take a deep dive into the world of cloud-based 
 Kubernetes and showcase the utility of containerized workflows for enabli
 ng enterprise-grade bioinformatics workflows in the cloud. Plus\, we’ll d
 emonstrate how cloud data lake are perfect for storing the immense amount
  of -omics data that life science orgs need to manage.
DTEND:20240524T094500
DTSTAMP:20260413T034932Z
DTSTART:20240524T093000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Building Enterprise-Grade Bioinformatics Pipelines using Cloud-Sca
 le Kubernetes
UID:SZSESSION634838
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Zachary Charlop-Powers\n\nRecap of the power and chal
 lenges of using NextFlow for bioinformatic workflow creation across three
  different companies in the (meta-) genome and synbio space.
DTEND:20240524T100000
DTSTAMP:20260413T034932Z
DTSTART:20240524T094500
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Nextflow In Synthetic Biology and Natural Product Discovery
UID:SZSESSION676387
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Nils Homer\n\n Fastquorum is a nf-core Nextflow pipel
 ine to produce UMI-based consensus sequencing reads from raw FASTQs for p
 owerful error-correction to improve sequencing adapters.  Individual libr
 ary molecules are tagged with unique molecular identifiers (UMIs) prior t
 o amplification\, such that multiple observations of each library molecul
 e can be made.  In some cases\, both strands of a double-stranded library
  molecule may be observed and uniquely tagged.  These tags (UMIs) are lev
 eraged to identify individual sequencing reads that observe the same libr
 ary source molecule to correct sequencing error and post-tagging error (e
 .g. PCR error and oxidative damage during library preparation)\, yielding
  high-accuracy consensus reads for use in low frequency variant detection
  and other applications.
DTEND:20240524T101500
DTSTAMP:20260413T034932Z
DTSTART:20240524T100000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Fastquorum: the fgbio best-practices for UMI-based consensus calli
 ng from raw FASTQs
UID:SZSESSION649697
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Andrew Stiles\n\nRefTrace is a tool for static analys
 is of Nextflow pipelines. This session will introduce the tool & cover co
 ding techniques attendees can use -- not only with RefTrace -- to make th
 eir pipelines more robust.
DTEND:20240524T103000
DTSTAMP:20260413T034932Z
DTSTART:20240524T101500
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Static Code Analysis of Nextflow Pipelines
UID:SZSESSION650256
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Angel Pizarro\n\nDeploying Nextflow workflows on the 
 cloud is just one part of the overall developer and operating experience.
  In this session\, we'll take a deep dive into infrastructure considerati
 ons to help you maximize the price and performance of running your workfl
 ows on AWS.
DTEND:20240524T110000
DTSTAMP:20260413T034932Z
DTSTART:20240524T103000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:What to know about and where to look for it when running Nextflow 
 on the cloud
UID:SZSESSION667871
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Coffee and pastries.
DTEND:20240524T113000
DTSTAMP:20260413T034932Z
DTSTART:20240524T110000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Coffee break
UID:SZSESSION9025f9a5-134b-462d-9292-66ee5d55638e
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Rob Syme\n\nInteractive analysis and visualization of
  outputs from secondary data analysis\, such as genomic alignments\, vari
 ant calls\, single-cell quantifications\, or microscopy images is critica
 l for biological interpretation and to confirm or refute experimental hyp
 otheses. Data Studios is a new feature on the Seqera Platform where you c
 an host a combination of container images and compute environments for in
 teractive analysis using your preferred tools\, like Jupyter notebooks\, 
 RStudio\, and Visual Studio Code IDEs.\n\nRob will showcase real-world ex
 amples to highlight how Data Studios can augment Nextflow workflows to en
 able end-to-end data analysis within the Seqera Platform.
DTEND:20240524T120000
DTSTAMP:20260413T034932Z
DTSTART:20240524T113000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Practical Data Studios
UID:SZSESSION663488
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speakers: Edgardo Sanabria-Valentín\, Geraldine Van der Auwera
 \, Irina Silva\, Lyndon Mitnaul\n\nWe all know the workforce in US biotec
 h today is far from representative of the US population. This panel will 
 focus on one critical dimension of this multifaceted problem: ensuring eq
 uitable opportunities and support for first-generation students in biotec
 h.\n\nFirst-generation students are individuals who are the first in thei
 r families to attend college or university\, meaning none of their parent
 s or guardians have completed a bachelor's degree. As trailblazers in the
 ir families\, they typically lack the familial guidance and support that 
 comes from having parents who have experienced college themselves\, which
  makes it more difficult for them to navigate the higher education system
 . They also often share intersecting identities with racially minoritized
  groups\, which can compound the difficulties they face. This amounts to 
 a myriad of challenges\, including financial constraints\, imposter syndr
 ome that manifests as feelings of not belonging or inadequacy\, limited a
 ccess to resources such as networking opportunities and academic support\
 , and navigating complex bureaucratic processes within educational instit
 utions. \n\nAll these challenges create inequitable barriers to academic 
 success\, professional development\, and overall well-being of first-gene
 ration students\, contributing substantially to the continued lack of div
 ersity in the workforce. \n\nThis makes it crucial to implement targeted 
 interventions and support systems to ensure equitable access to opportuni
 ties for first-generation students\, and success in their academic and ca
 reer pursuits. Importantly\, this is not solely the responsibility of tea
 ching institutions\; research institutions and commercial companies have 
 an important role to play in making that happen.\n\nOur panelists will dr
 aw from their extensive professional experience to discuss effective stra
 tegies and constructive approaches that organizations across the biotech 
 ecosystem can participate in to diversify the pipeline and foster first-g
 eneration success in biotech.\n\n\n\n
DTEND:20240524T124500
DTSTAMP:20260413T034932Z
DTSTART:20240524T120000
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Diversifying the pipeline: Fostering first-gen success in biotech
UID:SZSESSION658657
END:VEVENT
BEGIN:VEVENT
DESCRIPTION:Speaker: Evan Floden
DTEND:20240524T130000
DTSTAMP:20260413T034932Z
DTSTART:20240524T124500
LOCATION:Hackathon
SEQUENCE:330359
STATUS:CONFIRMED
SUMMARY:Closing remarks
UID:SZSESSION658614
END:VEVENT
END:VCALENDAR