Awesome List Updates on Jan 19, 2023

13 awesome lists updated today.

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1. Awesome Agi Cocosci

Problem Solving / Human-Level Problem Solving

• Hierarchical reasoning by neural circuits in the frontal cortex - Science, 2019. [All Versions]. Neuroscience evidence supporting rule switch.

• The importance of mixed selectivity in complex cognitive tasks - Nature, 2013. [All Versions]. The original paper introducing mixed selectivity with high-dimensional neural representations.

• Abstract strategy learning underlies flexible transfer in physical problem solving - CogSci'20, 2020. [All Versions].

Theory of Mind / AI Assisted Research

• The naïve utility calculus: Computational principles underlying commonsense psychology - Trends in Cognitive Sciences, 2016. [All Versions]. A perspective on understanding social interactions through the naïve utility calculus framework.

• Planning with theory of mind - Trends in Cognitive Sciences, 2022. [All Versions]. A perspective on understanding Theory of Mind through planning that consists of abstract structured causal representations and supports efficient search and selection from innumerable possible actions.

2. Awesome Gatling

Tools / Sandbox

• gatling-scaffold (⭐18) - Base for load test project using Gatling, InfluxDB and Grafana.

• perfiz (⭐15) - A dockerised API performance test setup based on Gatling with Grafana dashboards and Prometheus monitoring.

3. Awesome Privacy

Link in Bio Tools

• Keyoxide - A modern, secure and privacy-friendly platform to establish your decentralized online identity.

4. Awesome Rust

Applications / Text editors

• emacs-ng (⭐1.7k) - Complementing the C codebase with rust code to introduce new features.

• Lapce (⭐34k) - A modern editor with a backend. Taking inspiration from the discontinued xi-editor (⭐20k).

Libraries / GUI

• xilem (⭐3.4k) - Successor of the data-first UI design toolkit druid (⭐9.5k).

5. Awesome Cytodata

Datasets / Chemical Perturbations

• Haghighi et al. 2021 - Cell painting matched to L1000 profiles in 4 experiments, including compound and genetic screens (Details on GitHub (⭐42)).

Software / Genetic Perturbations

• histoCAT (⭐0) - Toolbox to extract quantitative phenotypic descriptors and contextual information for histology and multiplex imaging.

Publications / Reviews

• Pooled genetic screens with image-based profiling - Review of the different modalities available for genetic screens and which ones are suitable for morphological profiling.

Publications / Applications

• Tales of 1,008 Small Molecules: Phenomic Profiling through Live-cell Imaging in a Panel of Reporter Cell Lines - Demonstrating the effects of polypharmacology in MOA prediction while offering solutions for overcoming it in future image-based profiling studies.

• Multiparametric phenotyping of compound effects on patient derived organoids - Profiling chemical effects on patient-derived organoids.

• The phenotypic landscape of essential human genes - Comparing morphological descriptors in a pooled CRISPR screen with in-situ sequencing

• The molecular architecture of cell cycle arrest - Comparing cellular features across stages of the cell cycle.

• Integrated intracellular organization and its variations in human iPS cells - Decomposing cellular and nuclear shapes in 3D in multiple iPSC and studying association between cellular structures.

• Single-cell metabolic profiling of human cytotoxic T cells - Combining metabolic profiling and spatial information to define immune subsets in tumor microenvironments.

• The single-cell pathology landscape of breast cancer - Defining cell populations and their interactions in breast cancer based on shape, intensity and contextual information from multiplexed imaging.

• Identification of phenotype-specific networks from paired gene expression–cell shape imaging data - Looking for gene networks underlying cellular morphology by matching expression and imaging data.

• Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic - Model cell morphology with autoencoders to estimate effects of drug combinations.

• Deep Morphology Learning Enhances Ex Vivo Drug Profiling-Based Precision Medicine - Concrete description of how morphological information can be extracted from patient material and guide treatment.

Publications / Methods

• Label-Free Prediction of Cell Painting from Brightfield Images - Reconstructing images for Cell Painting dyes and ensuring corresponding morphological measurements are preserved.

• ShapoGraphy: A User-Friendly Web Application for Creating Bespoke and Intuitive Visualisation of Biomedical Data - Method to visualize morphological profiles.

• Morphology and gene expression profiling provide complementary information for mapping cell state - Comparison of the information contained in Cell Painting and L1000 assays for the same perturbations.

• Fully unsupervised deep mode of action learning for phenotyping high-content cellular images - Unsupervised approach to represent cellular morphology with clusters corresponding to meaningful relations such as mechanism of action. With an overview of deep learning methods for morphological profiling and classification.

• Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification - Experimental and computational workflow to extract 3D morphological descriptors of organoids using light-sheet microscopy.

6. Awesome No Login Web Apps

Programming Tools / Others

• DebugBear Speed Test - Test site speed and Core Web Vitals.

7. Awesome Generative Deep Art

Text-related Generative Tools / Multi-agents

• Character.AI: platform for creating and talking to advanced AI Characters

8. Awesome Selfhosted

Software / Wikis

• Wiki.js - Modern, lightweight and powerful wiki app using Git and Markdown. (Demo, Source Code (⭐24k)) AGPL-3.0 Nodejs/Docker/K8S

9. Awesome Electronics

PCB Batching Services / Altium

• PCBWay - Low cost PCB batching service with PCBA, CNC and 3D-Printing services.

10. Awesome Svelte

State Libraries

• Svelte-Domain (⭐5) - The state management for svelte.

• svelte-asyncable (⭐168) - The Svelte store contract with support for asynchronous values.

Miscellaneous / Checkbox

• mathjax-svelte (⭐0) - A Svelte component for MathJax.

11. Awesome Nextjs

Articles

• Guaranteeing webhook delivery in NextJS Application

12. Awesome Zsh Plugins

Themes / superconsole - Windows-only

• gianu-alternative (⭐1) - An alternative to OMZ Gianu (⭐172k) that changes prompt based on privilege. Includes git status and current directory decorators.

13. Free Programming Books (English, By Subjects)

Mathematics For Computer Science

• Graph Theory Exercises - Paulo Feofiloff (PDF)

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