35,091 research outputs found
Permanently : Preservation Lab Treatment Report
No full textThis is a 4 volume set of books by author Kenneth Koch, printed by Tiber Press in 1960. This set came to the Preservation Lab for rehousing. The books are in good condition, yet suffer from minor surface dirt. The original slip case designed for the book is missing, but a photo of the original was used as reference.View Catalog Record</a
Sen-Lab-LMS/Senescence_nuclear_features: Publication_version_2.0
No full text<p>Author checklist.</p>
Boxcar Poems, 1-12 : Preservation Lab Treatment Report
No full textThis is a small hardback meander book containing poems by John Dorsey. According to the colophon, the book was printed as a broadside and folded, torn and bound as a hardback meander book. The text was letterpress printed. Along with the book, there are four advertisement paper cards related to the author and the printing company. These were loosely set inside the book. This book came to the Lab for housing.View Catalog Record: http://uclid.uc.edu/record=b877704
geem-lab/overreact: v1.2.0
No full text⚛️ overreact is a library and a command-line tool for building and analyzing homogeneous microkinetic models from first-principles calculations.
This is a feature release of overreact that, among other minor changes, improves integrator stability and parameter choices for the integrators overall. In particular, overreact now makes similar choices to scipy.integrate.solve_ivp, which should lead to fewer surprises. A big part of this was kindly contributed by @bmounssefjr.
⚠️ It was found out that the currently calculated analytical Jacobian leads to problems, which is most relevant when implicit integrators are employed. This affects LSODA, Radau and BDF. As such, the usage of analytical Jacobians has been disabled for this version until we find a fix for the bug. Even though it is a breaking chance per se, it is mild, as most of the change happened in places where user had previously no access. We hope to fix this issue soon. Previous and published results were not affected.
Update it using pip:
$ pip install -U 'overreact[cli,fast]'
Overreact is licensed under the MIT license.
If you use overreact in your research, please cite:
Schneider, F. S. S.; Caramori, G. F. Overreact, an in Silico Lab: Automative Quantum Chemical Microkinetic Simulations for Complex Chemical Reactions. Journal of Computational Chemistry 2022, 44 (3), 209–217. doi:10.1002/jcc.26861.
Here's the reference in BibTeX format:
@article{overreact_paper2022,
title = {Overreact, an in silico lab: Automative quantum chemical microkinetic simulations for complex chemical reactions},
author = {Schneider, Felipe S. S. and Caramori, Giovanni F.},
year = {2022},
month = {Apr},
journal = {Journal of Computational Chemistry},
publisher = {Wiley},
volume = {44},
number = {3},
pages = {209–217},
doi = {10.1002/jcc.26861},
issn = {1096-987x},
url = {http://dx.doi.org/10.1002/jcc.26861},
}
What's Changed
Add basic issue templates by @schneiderfelipe in https://github.com/geem-lab/overreact/pull/378
Enforce ruff rules by @schneiderfelipe in https://github.com/geem-lab/overreact/pull/392
Improve integrator stability by @schneiderfelipe in https://github.com/geem-lab/overreact/pull/416
Bump scipy to 1.10.1 by @dependabot in https://github.com/geem-lab/overreact/pull/371
Bump markdown-it-py to 2.2.0 by @dependabot in https://github.com/geem-lab/overreact/pull/372
Bump matplotlib to 3.7.1 by @dependabot in https://github.com/geem-lab/overreact/pull/385
Bump flynt to 0.78 by @dependabot in https://github.com/geem-lab/overreact/pull/397
Bump jaxlib to 0.4.7 by @dependabot in https://github.com/geem-lab/overreact/pull/402
Bump black to 23.3.0 by @dependabot in https://github.com/geem-lab/overreact/pull/403
Bump jax to 0.4.8 by @dependabot in https://github.com/geem-lab/overreact/pull/405
Bump ipython to 8.12.0 by @dependabot in https://github.com/geem-lab/overreact/pull/404
Bump debugpy to 1.6.7 by @dependabot in https://github.com/geem-lab/overreact/pull/410
Bump mypy to 1.2.0 by @dependabot in https://github.com/geem-lab/overreact/pull/411
Bump rich to 13.3.4 by @dependabot in https://github.com/geem-lab/overreact/pull/413
chore(deps-dev): bump pytest to 7.3.1 by @dependabot in https://github.com/geem-lab/overreact/pull/414
chore(deps): bump thermo to 0.2.24 by @dependabot in https://github.com/geem-lab/overreact/pull/420
chore(deps-dev): bump pdoc to 13.1.1 by @dependabot in https://github.com/geem-lab/overreact/pull/419
chore(deps-dev): bump types-setuptools to 67.7.0.0 by @dependabot in https://github.com/geem-lab/overreact/pull/418
chore(deps-dev): bump ruff to 0.0.263 by @dependabot in https://github.com/geem-lab/overreact/pull/421
Full Changelog: https://github.com/geem-lab/overreact/compare/v1.1.0...v1.2.
Noisy Nora artwork : Preservation Lab Treatment Report
No full textAcclaimed author and illustrator, Rosemary Wells, has written many endearing children’s books including Noisy Nora (a story about a mischievous young mouse). As part of Ms. Well’s initiative, Real Art for Young Artists, in 2019, Rosemary Wells generously donated more than a dozen original illustrations for long‐term display at the Public Library of Cincinnati and Hamilton County. The opening for the exhibition is September 15th, 2019 at 2pm at the Children’s Library in the Main building downtown. The newly acquired illustrations are drawn in pen and India ink. There are 16 drawings (26 x 38 cm or smaller) and one booklet containing 8 pages (16 x 12 cm). To prepare the materials for long‐term exhibition, the Preservation Lab worked with numerous colleagues to carefully balance preservation standards with viewer’s needs, while also striving to maintain the artist’s intended interpretation of their work.View Catalog Record</a
Reconstructing the Union - Report of the 2017 CEPS Ideas Lab. CEPS Report, 12 May 2017
No full text"Reconstructing the Union" was the ambitious but timely theme of CEPS’ fourth big forum for debate, the Ideas Lab, which was held in Brussels, 23-24 February 2017. Experts from 11 policy domains shared their insights on the many complex challenges facing Europe. A total of 834 participants attended the event over the two days. This report gives an overview of the insights gleaned from the many constructive discussion
cmrglab/ExerciseModel: Exercise Signaling ODE Model
No full text<p>Updated code for Fowler <em>et al</em> (2024) exercise signaling model, pre-publication release for article in review at <em>Experimental Physiology</em></p>
cmrglab/GENEode: GENEode Release containing new supplemental data
No full text<p>Contains Supplemental Data for
Shulin Cao, Kyle S. Buchholz, Philip Tan, Jennifer C. Stowe, Ariel Wang, Annabelle Fowler, Katherine R. Knaus, Ali Khalilimeybodi, Alexander C. Zambon, Jeffrey H. Omens, Jeffrey J. Saucerman, Andrew D. McCulloch (2024) Differential Sensitivity to Longitudinal and Transverse Stretch Mediates Transcriptional Responses in Mouse Neonatal Ventricular Myocytes. Am J Physiol (Heart Circ Physiol)</p>
geem-lab/overreact: v1.1.0
No full text⚛️ overreact is a library and a command-line tool for building and analyzing homogeneous microkinetic models from first-principles calculations.
This is a feature release of overreact that improves output, automatic choice of most parameters and adds support for Python 3.10.
Update it using pip:
$ pip install -U 'overreact[cli,fast]'
Overreact is licensed under the MIT license.
ℹ️ By the way, our manuscript has been featured in the latest issue of the Journal of Computational Chemistry! If you use overreact in your research, please cite:
Schneider, F. S. S.; Caramori, G. F. Overreact, an in Silico Lab: Automative Quantum Chemical Microkinetic Simulations for Complex Chemical Reactions. Journal of Computational Chemistry 2022, 44 (3), 209–217. doi:10.1002/jcc.26861.
Here's the reference in BibTeX format:
@article{overreact_paper2022,
title = {Overreact, an in silico lab: Automative quantum chemical microkinetic simulations for complex chemical reactions},
author = {Schneider, Felipe S. S. and Caramori, Giovanni F.},
year = {2022},
month = {Apr},
journal = {Journal of Computational Chemistry},
publisher = {Wiley},
volume = {44},
number = {3},
pages = {209–217},
doi = {10.1002/jcc.26861},
issn = {1096-987x},
url = {http://dx.doi.org/10.1002/jcc.26861},
}
What's Changed
Highlights
It just works®:
overreact is easier than ever. We fine-tuned the choice of many parameters, so that your simulations run smoothly right from the start. It is now smart enough to guess for how long to simulate (bde5bece7a12adda2b43ff6cbce919d5bf886cb7, 3c842a7eb38ae5190925b33507955fa6e31c99c8), which solver to use (928b48d6226d08031cc313ef192bba567f343d4b), how fast should an equilibrium be (3a516bd80078044bf5863e766c03cce92031d2b0, 1d2cbc8616057f595e8cc31ce2eb1d1568c4db6a, 645578c3cea49f5efb27cc1b8f2d5098bbd4d4bf), how to handle edge cases when correcting for quantum tunneling (0e5ad845a7eb6565aba67e45f3fa7e8d273a262b), which species actually make sense to plot when generating a kinetic profile (2de3dbd24e885786cce2d73a4bd9c311a8a3ce75), how large show the first time step be in a simulation (8eafc35bce452345a530c67a42476a1a284f1384, a4cd60d6cd2ebda62e3314940af9e671880541ee, ae55264300b8d0e13626f8c6fb6000e16f48fa45), and more.
Adjust energies per species:
You can now use the extra_energy_term flag to adjust the energy of a single species (777155ce15d69492a10dce401c8138e9d7eb6c73).
User-interface and output:
The output has been enhanced and is clearer than ever (13fd9ae3b48fecf98a7c84688206101387cf9826, 4f2c0d4a28c9f9a0fd12dca061483348ecdcd86e, dec2297ba8020b12eab10d48fcc666756760a0b9), which now shows the progress of the calculation as it is being performed (2d4d894d043053b203d495932c800ef45bd0c1c5). Error messages and warnings have been improved as well (92c7cb0fd3da1b09fee70ae002ce59b596a227c5).
Documentation and resources:
We greatly improved consistency between the documentation, API and command-line help (f0bc3b93a7c8bfae6a2c2564ff331ed43c72e7ec, d828d379f97342489301b2893eea677f3b5da3d5, 0ae47270f46a1709cb9776125bb2013058d81882, 1a2d0305894e57287d70fe827c0b0825095d448f, c6daa5502ff7d0e00e9e0541d1fcc066a5e1a1e9). In fact, we now have two sets of documentations: the user guide, focused on the use of the command-line application, and the Python API documentation (b1c745671f10c201b02b2122c9a8b60695f97a98, 4ecacfc23faf5b83cef58545408ca809e6e235fe, ea298d0acb56608620e1bfaa608dd79502ad8cac, 8ca1c7fe110f26d6b47f3777ee159ceba335c206, b6c888658fbf63d901b4e1fb59ba8469ece8d8df, da221515660542264ca6cee53c7414712d2dde4c, 8eb5f06386d5eedb4510f35e06a7b07f6db8a1ce, 0212376214b27b49a1fbc7cd53942f2ddef9cb86). We now have an improved README.md file (79ba5f2010e2b581ba2c943af54cb7c3bad235f0, df904083c8fb0536e7dc483222ae9b2053f257b5, c2b62edb609a01096e1c9b44694f90e49d731472, 0be2ad8392112b8afc79682e8f7f24b695434f5c, 64da6b9954f9dfec7f8f10c77dffeaf6d7176194, #149), as well as a great CONTRIBUTING.md thanks to @Leticia-maria (fcccbd174bbd8e56bca6c5a0eb3c4350972c42d3, f1ce7c0f7b06d5245d5d3daa0450f35a797f5716, #133). Thanks, Letícia!
Code quality and API:
The user-facing API is now almost completely type-hinted (37cca8d2217b5fcc812f26ed793543f235ac42f7, 819773c1ccf83dd36d06939d94584c2e6810f6d3). There might be some rough edges yet, so feel free to open an issue if you see something. Lots of housekeeping has been taken place as well, mostly to keep the code base modern, performant, and easy to use (f47206b07787fc074dbfd5bded9e87e1d2f882e7, ea27d5b234d5ed972d6283340a342ccd040fccf9, 2f6a176d5bd513ad0e50aac0e12e9c3ee92d588f, fb99f6c9d24dd26fe62d289f70e76f0e6d0acac1, 7622789e029bc3fd4ab660c25e3939f929de740b, f60a705ca184bebd845401b8c9925dc49e32cc09). We now target Python versions 3.8-3.10 (bc67e7de1ddbb30fe541f4883c10eaacaded7131, c0892441194ee0d8b2f5eaf8294d7c5023eef2ac), and use Ruff and Black to keep the code base as tidy as possible (cddc09d5d8c877abee16ac14de2e38869a73bc2a, a0f1be3648a0c1cf7ebf97c60dbc622020b224d8, 14dde8662ba9fa6285d01c9ae59ffc56134a5e81).
Pull requests
Here are the list of relevant pull requests since last version.
Update CONTRIBUTING.md by @Leticia-maria in https://github.com/geem-lab/overreact/pull/133
Add table to organize badges by @Leticia-maria in https://github.com/geem-lab/overreact/pull/149
Bump actions/checkout from 2 to 3 by @dependabot in https://github.com/geem-lab/overreact/pull/182
Bump bandit from 1.7.3 to 1.7.4 by @dependabot in https://github.com/geem-lab/overreact/pull/184
Bump codecov/codecov-action from 2 to 3 by @dependabot in https://github.com/geem-lab/overreact/pull/213
Bump github/codeql-action from 1 to 2 by @dependabot in https://github.com/geem-lab/overreact/pull/227
Bump thermo from 0.2.20 to 0.2.21 by @dependabot in https://github.com/geem-lab/overreact/pull/240
Bump pillow from 9.1.0 to 9.1.1 by @dependabot in https://github.com/geem-lab/overreact/pull/251
Bump notebook from 6.4.11 to 6.4.12 by @dependabot in https://github.com/geem-lab/overreact/pull/257
Bump abatilo/actions-poetry from 2.1.4 to 2.1.6 by @dependabot in https://github.com/geem-lab/overreact/pull/282
Bump nbconvert from 6.5.0 to 6.5.1 by @dependabot in https://github.com/geem-lab/overreact/pull/283
Bump mistune from 0.8.4 to 2.0.3 by @dependabot in https://github.com/geem-lab/overreact/pull/290
Bump cclib from 1.7.1 to 1.7.2 by @dependabot in https://github.com/geem-lab/overreact/pull/288
Bump flake8 from 4.0.1 to 5.0.4 by @dependabot in https://github.com/geem-lab/overreact/pull/292
Bump pytest from 7.1.2 to 7.1.3 by @dependabot in https://github.com/geem-lab/overreact/pull/297
Bump actions/setup-python from 4.2.0 to 4.3.0 by @dependabot in https://github.com/geem-lab/overreact/pull/306
Bump pytest-cov from 3.0.0 to 4.0.0 by @dependabot in https://github.com/geem-lab/overreact/pull/314
Bump matplotlib from 3.6.1 to 3.6.2 by @dependabot in https://github.com/geem-lab/overreact/pull/319
Bump mypy from 0.990 to 0.991 by @dependabot in https://github.com/geem-lab/overreact/pull/328
Bump pdoc from 12.2.2 to 12.3.0 by @dependabot in https://github.com/geem-lab/overreact/pull/329
Bump debugpy from 1.6.3 to 1.6.4 by @dependabot in https://github.com/geem-lab/overreact/pull/336
Bump flynt from 0.76 to 0.77 by @dependabot in https://github.com/geem-lab/overreact/pull/335
Bump types-setuptools from 65.6.0.1 to 65.6.0.2 by @dependabot in https://github.com/geem-lab/overreact/pull/340
Bump pyupgrade from 3.3.0 to 3.3.1 by @dependabot in https://github.com/geem-lab/overreact/pull/341
Bump black from 22.10.0 to 22.12.0 by @dependabot in https://github.com/geem-lab/overreact/pull/342
Bump jax from 0.3.25 to 0.4.1 by @dependabot in https://github.com/geem-lab/overreact/pull/346
Bump jaxlib from 0.3.25 to 0.4.1 by @dependabot in https://github.com/geem-lab/overreact/pull/345
Bump isort from 5.11.3 to 5.11.4 by @dependabot in https://github.com/geem-lab/overreact/pull/348
Bump seaborn from 0.12.1 to 0.12.2 by @dependabot in https://github.com/geem-lab/overreact/pull/350
Bump rich from 12.6.0 to 13.0.0 by @dependabot in https://github.com/geem-lab/overreact/pull/349
Bump scipy from 1.9.3 to 1.10.0 by @dependabot in https://github.com/geem-lab/overreact/pull/351
Bump ipython from 8.7.0 to 8.8.0 by @dependabot in https://github.com/geem-lab/overreact/pull/352
New Contributors
@Leticia-maria made their first contribution in https://github.com/geem-lab/overreact/pull/133
Full Changelog: https://github.com/geem-lab/overreact/compare/v1.0.2...v1.1.
cmrglab/ExerciseModel: ExerciseModel: Exercise Signaling ODE Model
No full text<p>Updated data tables and code for Fowler et al (2023) exercise signaling model, pre-publication release for article in review at Experimental Physiology</p>
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