The Lifespan Machine v2

Nicholas Stroustrup Centre for Genomic Regulation http://lifespanmachine.crg.eu

This repository contains v2 of the lifespan machine software, comprised of

1. Scanner control software ( ns_image_server ) for the distributed high-throughput microscope system first described in Stroustrup et al. "The C. elegans Lifespan Machine". Nature Methods 2013
2. Image analysis software ( ns_image_server ) that extracts survival data from lifespan machine data sets
3. Visualization software ( ns_worm_browser ) for inspecting and annotating images and automated analysis.

For additional documentation, please take a look at:

• The software installation guide: doc/lifespan_machine_software_installation.pdf
• The software tutorial: doc/lifespan_machine_software_tutorial.pdf
• The 2013 methods paper: doc/nmeth.2475.pd
• The 2013 methods paper supplement: nmeth.2475-S1.pdf
• The 2021 methods update paper: https://doi.org/10.1101/2021.03.31.437415

Copyright 2022 Reservation of Rights All Rights Reserved

Major Revisions

2020.08.29: version 2.5 is finished and merged into the v2 branch. This update adds feature-complete support for the new hidden markov model (HMM) posture analysis models, upgrades to the worm browser UI, and many bugfixes.

2019.08.01: version 2.3 is finished and merged into the v2 branch. This update contains major user interface performance improvements in the worm browser, performance upgrades, and many bugfixes.

2018.08.01: version 2 is declared stable

2017.08.02: version 2 beta is ready for testing

2013.2.24: First commit to github

2006.10.17: Start of project

Some publications that have used the Lifespan Machine Software

Sen, Ilke, et al. "DAF-16/FOXO requires Protein Phosphatase 4 to initiate transcription of stress resistance and longevity promoting genes." Nature communications 11.1 (2020): 1-17.

Schiffer, Jodie A., et al. "Caenorhabditis elegans processes sensory information to choose between freeloading and self-defense strategies." Elife 9 (2020): e56186. Bazopoulou, Daphne, et al. "Developmental ROS individualizes organismal stress resistance and lifespan." Nature 576.7786 (2019): 301-305.

Guerrero-Rubio, M. Alejandra, et al. "Extension of life-span using a RNAi model and in vivo antioxidant effect of Opuntia fruit extracts and pure betalains in Caenorhabditis elegans." Food chemistry 274 (2019): 840-847.

Janssens, Georges E., et al. "Transcriptomics-based screening identifies pharmacological inhibition of Hsp90 as a means to defer aging." Cell reports 27.2 (2019): 467-480. Kasimatis, Katja R., Megan J. Moerdyk-Schauwecker, and Patrick C. Phillips. "Auxin-mediated sterility induction system for longevity and mating studies in Caenorhabditis elegans." G3: Genes, Genomes, Genetics 8.8 (2018): 2655-2662.

Lin, Xin-Xuan, et al. "DAF-16/FOXO and HLH-30/TFEB function as combinatorial transcription factors to promote stress resistance and longevity." Nature communications 9.1 (2018): 1-15.

Stroustrup, Nicholas, et al. "The temporal scaling of Caenorhabditis elegans ageing." Nature 530.7588 (2016): 103-107

Lucanic, Mark, et al. "Chemical activation of a food deprivation signal extends lifespan." Aging Cell 15.5 (2016): 832-841.

McEwan, Deborah L., et al. "Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway." BMC biology 14.1 (2016): 1-17.

de Abreu, Diana Andrea Fernandes, et al. "An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology." PLoS Genet 10.3 (2014): e1004225.

Banse, Stephen A., et al. "Automated lifespan determination across Caenorhabditis strains and species reveals assay-specific effects of chemical interventions." GeroScience 41.6 (2019): 945-960.

Software Copyright 2021 Reservation of Rights All Rights Reserved