bakirillov

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.

bakirillov

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

bakirillov

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

bakirillov

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)

bakirillov

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

bakirillov

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]. 

bakirillov

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.

bakirillov

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

bakirillov

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

bakirillov

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