September 2021 - talks - lists.cs.princeton.edu

Best Practices in Python Packaging - NOW OFFERING ZOOM OPTION
by Emily C. Lawrence 28 Sep '21

28 Sep '21

Now offering in person (for Princeton affiliates only) and Zoom webinar (non-Princeton and off-campus Princeton affiliates): REGISTRATION IS REQUIRED FOR BOTH Attending in person: [ https://docs.google.com/forms/d/e/1FAIpQLSetxqgVqlgnNQwHKJ-IFA_V84gY2YxFip_… | REGISTER HERE ] Zoom webinar: [ https://princeton.zoom.us/webinar/register/WN_NIQuLIkvQS-UlwnYdywGRA | ZOOM WEBINAR REGISTER HERE ] DataX Workshop Series: Best Practices in Python Packaging [ https://csml.princeton.edu/news/datax-brian-arnold-using-data-science-answe… | Brian Arnold ] , DataX Biomedical Data Scientist [ https://csml.princeton.edu/news/solving-technical-debt-dilemma-princetons-m… | Vineet Bansal ] , Sr. Research Software Engineer October 1, 2021 9:00 am Location: 26 Prospect Avenue, Room 103 Seating is limited – please reserve your spot early! This workshop is for researchers who are already using Python for their work, but who want to distribute their software to the broader scientific community by packaging their code for other researchers to easily use. We will learn about structuring our code as modules and packages, and publishing packages on PyPI and conda, both of which are commonly used in the life sciences to install open-source software. We will gain insights into ensuring reproducibility in research through the process of versioning, continuous integration and testing. Finally, we will look at a sample Python project that puts all these best practices together. [ https://docs.google.com/forms/d/e/1FAIpQLSetxqgVqlgnNQwHKJ-IFA_V84gY2YxFip_… | REGISTER HERE ]

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NEXT FRIDAY WORKSHOP: Best Practices in Python Packaging
by Emily C. Lawrence 22 Sep '21

22 Sep '21

DataX Workshop Series: Best Practices in Python Packaging [ https://csml.princeton.edu/news/datax-brian-arnold-using-data-science-answe… | Brian Arnold ] , DataX Biomedical Data Scientist [ https://csml.princeton.edu/news/solving-technical-debt-dilemma-princetons-m… | Vineet Bansal ] , Sr. Research Software Engineer October 1, 2021 9:00 am Location: 26 Prospect Avenue, Room 103 Seating is limited – please reserve your spot early! This workshop is for researchers who are already using Python for their work, but who want to distribute their software to the broader scientific community by packaging their code for other researchers to easily use. We will learn about structuring our code as modules and packages, and publishing packages on PyPI and conda, both of which are commonly used in the life sciences to install open-source software. We will gain insights into ensuring reproducibility in research through the process of versioning, continuous integration and testing. Finally, we will look at a sample Python project that puts all these best practices together. [ https://docs.google.com/forms/d/e/1FAIpQLSetxqgVqlgnNQwHKJ-IFA_V84gY2YxFip_… | REGISTER HERE ]

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Kathleen Chen will present her General Exam "A sequence-based global map of regulatory activity for deciphering human genetics" on Monday, September 27, 2021 at 11:30AM via Zoom
by jfarquer＠cs.princeton.edu 21 Sep '21

21 Sep '21

Kathleen Chen will present her General Exam "A sequence-based global map of regulatory activity for deciphering human genetics" on Monday, September 27, 2021 at 11:30AM via Zoom. Zoom Link: https://princeton.zoom.us/j/96378734253 The members of Kathleen's committee are as follows: Olga Troyanskaya (adviser), Mona Singh, Yuri Pritykin Title: A sequence-based global map of regulatory activity for deciphering human genetics Everyone is invited to attend the talk, and those faculty wishing to remain for the oral exam following are welcome to do so. Abstract: Sequence is at the basis of how the genome shapes chromatin organization, regulates gene expression, and impacts traits and diseases. Epigenomic profiling efforts have enabled large-scale identification of regulatory elements, yet we still lack a sequence-based map to systematically identify regulatory activities from any sequence, which is necessary for predicting the effects of any variant on these activities. We address this challenge with Sei, a new framework for integrating human genetics data with sequence information to discover the regulatory basis of traits and diseases. Our framework systematically learns a vocabulary for the regulatory activities of sequences, which we call sequence classes, using a new deep learning model that predicts a compendium of 21,907 chromatin profiles across >1,300 cell lines and tissues, the most comprehensive to-date. Sequence classes allow for a global view of sequence and variant effects by quantifying diverse regulatory activities, such as loss or gain of cell-type-specific enhancer function. We show that sequence class predictions are supported by experimental data, including tissue-specific gene expression, expression QTLs, and evolutionary constraints based on population allele frequencies. Finally, we applied our framework to human genetics data. Sequence classes uniquely provide a non-overlapping partitioning of GWAS heritability by tissue-specific regulatory activity categories, which we use to characterize the regulatory architecture of 47 traits and diseases from UK Biobank. Furthermore, the predicted loss or gain of sequence class activities suggest specific mechanistic hypotheses for individual regulatory pathogenic mutations. We provide this framework as a resource to further elucidate the sequence basis of human health and disease. Reading List: Textbook: Jones, N.C. and Pevzner, P.A. An Introduction to Bioinformatics Algorithms. Cambridge, MA: MIT Press (2004). Papers: 1. Zhou, J. et al. "Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk." Nat Genetics vol. 50,8 (2018): 1171-1179. doi:10.1038/s41588-018-0160-6 2. Zhou, J., Park, C.Y, et al. Theesfeld, C.L. et al. "Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk." Nat Genetics 51, 973-980 (2019). 3. Kelley, D.R., et al. "Sequential regulatory activity prediction across chromosomes with convolutional neural networks." Genome Res 28(5), 739-750 (2018). 4. Avsec et al. "Base-resolution models of transcription-factor binding reveal soft motif syntax." Nat Genetics 53, 354-366 (2021). 5. Edwards, S.L. et al. "Beyond GWASs: illuminating the dark road from association to function." American Journal of Human Genetics vol. 93,5 (2013): 779-97. 6. Boix, C.A. et al. "Regulatory genomic circuitry of human disease loci by integrative epigenomics." Nature 590, 300-307 (2021). 7. Chen et al. "Determinants of transcription factor regulatory range." Nat Communications 11, 2472 (2020). 8. Rheinbay E. et al. "Analyses of non-coding somatic drivers in 2,658 cancer whole genomes." Nature 578, 102-111 (2020). 9. Weissbrod O. et al. "Functionally informed fine-mapping and polygenic localization of complex trait heritability." Nat Genetics 52, 1355-1363 (2020).

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Comparative Literature talk: Dennis Tenen, 9/23 at 4:30PM
by Emily C. Lawrence 20 Sep '21

20 Sep '21

Dearest colleagues, The Department of Comparative Literature is proud to welcome Professor Dennis Tenen of Columbia University to give the first lecture in this year’s departmental lecture series. This year’s lecture series is entitled “Virtually Here, Virtually So ” and it aims at thinking through the many meanings of the word “virtual” i ncluding, but by no means limited to, virtual reality, things that are “virtually" the same yet profoundly different, and the similarities and discrepancies between our “true” selves and our “virtual” selves. Professor Tenen is the author of " Plain Text: The Poetics of Computation" (2017) and his work lies at the intersection of literary theory, new media studies, and coding studies. He will be presenting a lecture entitled “Media and Metaphor (Or How Literary Theory Figures in the Study of Human Computer Interaction)” on Thursday September 23rd at 4:30 PM in East Pyne 010 . The talk will be immediately followed by a small reception just outside of the auditorium. There are also limited spots available for dinner with Professor Tenen at 6:30 PM after the lecture at 6:30PM. If you are interested in joining us for dinner or have any questions or concerns, please address them to Daniel Dominguez ( [ mailto:dd10@princeton.edu | dd10(a)princeton.edu ] ). We hope everyone has a wonderful week and we sincerely hope you’ll join us this week to listen to Professor Tenen speak. Best wishes, Daniel Dominguez Series Organizer

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