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1. Anaïs Le Rhun, Andrés Escalera-Maurer, Majda Bratovič, and Emmanuelle Charpentier. Crispr-cas in streptococcus pyogenes. RNA biology, 16(4):380–389, 2019. | |
2. https://www.uniprot.org/uniprotkb/A0A2U3D0N8/entry | |
3. Yongmoon Jeon, You Hee Choi, Yunsu Jang, Jihyeon Yu, Jiyoung Goo, Gyejun Lee, You Kyeong Jeong, Seung Hwan Lee, In-San Kim, Jin-Soo Kim, et al.Direct observation of dna target searching and cleavage by crispr-cas12a. Nature communications, 9(1):2777, 2018. | |
4. Bogdan Kirillov, Ekaterina Savitskaya, Maxim Panov, Aleksey Y Ogurtsov, Svetlana A Shabalina, Eugene V Koonin, and Konstantin V Severinov. Uncertainty-aware and interpretable evaluation of cas9–grna and cas12a–grna specificity for fully matched and partially mismatched targets with deep kernel learning. Nucleic acids research, 50(2):e11–e11, 2022. |
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1. Anaïs Le Rhun, Andrés Escalera-Maurer, Majda Bratovič, and Emmanuelle Charpentier. Crispr-cas in streptococcus pyogenes. RNA biology, 16(4):380–389, 2019. | |
2. Kira S Makarova, Yuri I Wolf, Jaime Iranzo, Sergey A Shmakov, Omer S Alkhnbashi, Stan JJ Brouns, Emmanuelle Charpentier, David Cheng, Daniel H Haft, Philippe Horvath, et al. Evolutionary classification of crispr–cas systems: a burst of class 2 and derived variants. Nature Reviews Microbiology, 18(2):67–83, 2020. | |
3. Simon A Jackson, Rebecca E McKenzie, Robert D Fagerlund, Sebastian N Kieper, Peter C Fineran, and Stan JJ Brouns. Crispr-cas: adapting to change. Science, 356(6333):eaal5056, 2017. | |
4. Yongmoon Jeon, You Hee Choi, Yunsu Jang, Jihyeon Yu, Jiyoung Goo, Gye- jun Lee, You Kyeong Jeong, Seung Hwan Lee, In-San Kim, Jin-Soo Kim, et al. Direct observation of dna target searching and cleavage by crispr-cas12a. Na- ture communications, 9(1):2777, 2018. | |
5. Alkhnbashi, Omer S., et al. "CRISPRstrand: predicting repeat orientations to determine the crRNA |
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Kahl M. et al. Ultra-low-cost 3D bioprinting: modification and application of an off-the-shelf desktop 3D-printer for biofabrication //Frontiers in bioengineering and biotechnology. – 2019. – Т. 7. – С. 184. | |
Incucyte picture - https://medicine.tulane.edu/departments/biochemistry-molecular-biology/core-facilities/incucyte-sx5-live-cell | |
Pakhomova C. et al. Software for bioprinting //International Journal of Bioprinting. – 2020. – Т. 6. – №. 3. | |
Firedrake, used for solving the equations - https://www.firedrakeproject.org | |
PyVista, used for visualization - Sullivan et al., (2019). PyVista: 3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK). Journal of Open Source Software, 4(37), 1450, https://doi.org/10.21105/joss.01450 | |
Meshio, used to work with mesh files in Python - https://github.com/nschloe/meshio |
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from sdf import * | |
s = tetrahedron(0.75) | |
s = s.translate(Z * -3) | s.translate(Z * 3) | |
f = sphere(3).union( | |
s.orient(X), s.orient(Y), s.orient(Z), | |
s.orient(X+Y), s.orient(Y+Z), s.orient(X+Y+Z), | |
k=1 | |
) | |
d = box((30, 30, 2)).translate(Z*-2) |
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import os | |
import cv2 | |
import torch | |
import einops | |
import numpy as np | |
import pandas as pd | |
from torch import nn | |
import os.path as op | |
from torch.optim import Adam | |
import pytorch_lightning as pl |
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This is the visualization of an attempt to reproduce [5]. It shows the oxygen map for z=0. Notice the similarity with Figure 5 of [5]. |
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1. https://www.amazon.com/Creality-Official-Upgraded-Carborundum-220x220x250mm/dp/B087FDTV3X | |
2. https://phys.org/news/2020-07-bioink-cell-bioprinting-d.html?deviceType=mobile | |
3. https://news.yahoo.com/news/onvo-initiating-coverage-organovo-150000829.html | |
4. Pasko, Alexander, et al. "Function representation in geometric modeling: concepts, implementation and applications." The visual computer 11.8 (1995): 429-446. | |
5. Grimes, David Robert, and Frederick J. Currell. "Oxygen diffusion in ellipsoidal tumour spheroids." Journal of the Royal Society Interface 15.145 (2018): 20180256. | |
6. https://izicad.skoltech.ru | |
7. Geuzaine, Christophe, and Jean‐François Remacle. "Gmsh: A 3‐D finite element mesh generator with built‐in pre‐and post‐processing facilities." International journal for numerical methods in engineering 79.11 (2009): 1309-1331. | |
8. Rathgeber, Florian, et al. "Firedrake: automating the finite element method by composing abstractions." ACM Transactions on Mathematical Software (TOMS) 43.3 (2016): 1-27. |
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1. Fleming PA, Argraves WS, Gentile C, et al., 2010, Fusion of Uniluminal Vascular Spheroids: A Model for Assembly of Blood Vessels. Dev Dyn, 239:398–406. DOI: 10.1002/dvdy.22161. | |
2. Inamori M, Hiroshi M, Toshihisa K, 2009, An Approach for Formation of Vascularized Liver Tissue by Endothelial Cell-covered Hepatocyte Spheroid Integration. Tissue Eng Part A, 15:2029–2037. DOI: 10.1089/ten.tea.2008.0403.3. Rouwkema J, Khademhosseini A, 2016, Vascularization and Angiogenesis in Tissue Engineering: Beyond Creating Static Networks. Trends Biotechnol, 34:733–45. DOI: 10.1016/j.tibtech.2016.03.002. | |
4. Hoch E, Tovar GE, Borchers K, 2014, Bioprinting of Artificial Blood Vessels: Current Approaches Towards a Demanding Goal. Eur J Cardiothorac Surg, 46:767–78. DOI: 10.1093/ejcts/ezu242. | |
5. Alonzo M, AnilKumar S, Roman B, et al., 2019, 3D Bioprinting of Cardiac Tissue and Cardiac Stem Cell Therapy. Transl Res, 211:64–83. DOI: 10.1016/j.trsl.2019.04.004. | |
6. Lee W, Debasitis JC, Lee VK, et al,. 2009, M |
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FROM firedrakeproject/firedrake:latest | |
USER root | |
RUN rm /bin/sh && ln -s /bin/bash /bin/sh | |
RUN apt-get update && apt-get -y update | |
RUN apt-get install -y build-essential python3.6 python3-pip python3-dev | |
RUN pip3 -q install pip --upgrade | |
RUN pip3 install jupyter | |
RUN pip3 install matplotlib | |
RUN pip3 install numpy | |
RUN pip3 install scipy |
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1. E.Loper, S.Bird (2002) Nltk: The natural language toolkit. arXiv preprint arXiv:cs/0205028. | |
2. K.W.Church (2017) Word2Vec. Natural Language Engineering, 23(1):155-162. | |
3. J.H.Lau, T.Baldwin (2016) An empirical evaluation of doc2vec with practical insights into document embedding generation. arXiv preprint, arXiv:1607.05368. | |
4. C.R.Huang, P.Šimon, S.K.Hsieh, L.Prévot (2007) Rethinking chinese word segmentation: tokenization, character classification, or wordbreak identification. In Proceedings of the 45th Annual Meeting of the Association for Computational Linguistics Companion Volume Proceedings of the Demo and Poster Sessions, pp. 69-72. | |
5. E.Asgari, M.R.Mofrad (2015) Continuous distributed representation of biological sequences for deep proteomics and genomics. PloS one, 10(11):e0141287. | |
6. H.Iuchi et al (2021) Representation learning applications in biological sequence analysis. bioRxiv. | |
7. P.Ng (2017) dna2vec: Consistent vector representations of variable-length k-mers. arXiv preprint, arXiv:1701.06279 |
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