-
Notifications
You must be signed in to change notification settings - Fork 2
/
CITATION.cff
656 lines (643 loc) · 21.8 KB
/
CITATION.cff
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
# Citation File Format (cff).
# See https://citation-file-format.github.io/
cff-version: "1.2.0"
message: "If you use this software, please cite it using these metadata."
# Keep project metadata in sync with mdtools._metadata.py and
# AUTHORS.rst.
type: "software"
title: "MDTools"
abstract: >-
Python scripts to prepare and analyze molecular dynamics simulations.
authors:
- given-names: "Andreas"
family-names: "Thum"
alias: "andthum"
email: "[email protected]"
tel: "+49 251 83-29179"
fax: "+49 251 83-29159"
affiliation: "University of Münster, Institute for Physical Chemistry"
address: "Corrensstraße 28/30"
city: "Münster"
post-code: 48149
country: "DE"
region: "North Rhine-Westphalia"
orcid: "https://orcid.org/0000-0002-2262-8507"
- given-names: "Len"
family-names: "Kimms"
alias: "ezavod"
email: "[email protected]"
tel: "+49 251 83-29154"
fax: "+49 251 83-29159"
affiliation: "University of Münster, Institute for Physical Chemistry"
address: "Corrensstraße 28/30"
city: "Münster"
post-code: 48149
country: "DE"
region: "North Rhine-Westphalia"
orcid: "https://orcid.org/0000-0003-2769-923X"
contact:
- given-names: "Andreas"
family-names: "Thum"
email: "[email protected]"
identifiers:
- description: "The concept DOI of the software."
type: "doi"
value: "10.5281/zenodo.7615177"
url: "https://github.com/andthum/mdtools"
repository-code: "https://github.com/andthum/mdtools"
license: "GPL-3.0-or-later"
license-url: "https://www.gnu.org/licenses/gpl-3.0.html"
# TODO: Find a way to automatically update `commit`, `version` and
# `date-released`.
# commit: "40aea3299c1d1f15435e39c5385e7f3d25bac038"
# version: "0.0.0.dev2"
# date-released: "2021-06-26"
keywords:
- "Scripts Collection"
- "Python Scripts"
- "Science"
- "Scientific Computing"
- "Computational Science"
- "Computational Biology"
- "Computational Chemistry"
- "Computational Physics"
- "Materials Science"
- "Molecular Simulation"
- "Molecular Modeling"
- "Molecular Mechanics"
- "Molecular Dynamics"
- "Molecular Dynamics Simulation"
- "Trajectory Analysis"
- "MDAnalysis"
- "NumPy"
- "Python3"
- "GPLv3"
# Keep references in sync with requirements.txt.
references:
- type: "software"
title: "MDAnalysis"
abstract: >-
MDAnalysis is a Python library to analyze molecular dynamics simulations.
authors:
- given-names: "Naveen"
family-names: "Michaud-Agrawal"
- name: "The MDAnalysis Core Developer Team"
- name: "All Contributors to MDAnalysis"
url: "https://www.mdanalysis.org"
repository-code: "https://github.com/MDAnalysis/mdanalysis"
license: "GPL-2.0-or-later"
license-url: "https://www.gnu.org/licenses/gpl-2.0.html"
keywords:
- "python"
- "science"
- "chemistry"
- "biophysics"
- "molecular-dynamics"
- "computational-chemistry"
- "molecular-simulation"
- "analysis"
- "trajectory-analysis"
- type: "proceedings"
title: >-
MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics
Simulations
abstract: >-
MDAnalysis (http://mdanalysis.org) is a library for structural and
temporal analysis of molecular dynamics (MD) simulation trajectories and
individual protein structures. MD simulations of biological molecules
have become an important tool to elucidate the relationship between
molecular structure and physiological function. Simulations are performed
with highly optimized software packages on HPC resources but most codes
generate output trajectories in their own formats so that the development
of new trajectory analysis algorithms is confined to specific user
communities and widespread adoption and further development is delayed.
MDAnalysis addresses this problem by abstracting access to the raw
simulation data and presenting a uniform object-oriented Python interface
to the user. It thus enables users to rapidly write code that is portable
and immediately usable in virtually all biomolecular simulation
communities. The user interface and modular design work equally well in
complex scripted work flows, as foundations for other packages, and for
interactive and rapid prototyping work in IPython / Jupyter notebooks,
especially together with molecular visualization provided by nglview and
time series analysis with pandas. MDAnalysis is written in Python and
Cython and uses NumPy arrays for easy interoperability with the wider
scientific Python ecosystem. It is widely used and forms the foundation
for more specialized biomolecular simulation tools. MDAnalysis is
available under the GNU General Public License v2.
authors:
- given-names: "Richard J."
family-names: "Gowers"
- given-names: "Max"
family-names: "Linke"
- given-names: "Jonathan"
family-names: "Barnoud"
- given-names: "Tyler John Edward"
family-names: "Reddy"
- given-names: "Manuel N."
family-names: "Melo"
- given-names: "Sean L."
family-names: "Seyler"
- given-names: "Jan"
family-names: "Domanski"
- given-names: "David L."
family-names: "Dotson"
- given-names: "Sebastien"
family-names: "Buchoux"
- given-names: "Ian M."
family-names: "Kenney"
- given-names: "Oliver"
family-names: "Beckstein"
editors:
- given-names: "Sebastian"
family-names: "Benthall"
- given-names: "Scott"
family-names: "Rostrup"
conference:
name: "Proceedings of the 15th Python in Science Conference"
city: "Austin"
region: "Texas"
country: "US"
year: 2016
pages: 98-105
doi: "10.25080/Majora-629e541a-00e"
url: "https://www.osti.gov/biblio/1565806"
keywords:
- "software"
- "molecular dynamics simulations"
- "science"
- "chemistry"
- "physics"
- "biology"
- type: "article"
title: >-
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
abstract: >-
Abstract MDAnalysis is an object-oriented library for structural and
temporal analysis of molecular dynamics (MD) simulation trajectories and
individual protein structures. It is written in the Python language with
some performance-critical code in C. It uses the powerful NumPy package
to expose trajectory data as fast and efficient NumPy arrays. It has been
tested on systems of millions of particles. Many common file formats of
simulation packages including CHARMM, Gromacs, Amber, and NAMD and the
Protein Data Bank format can be read and written. Atoms can be selected
with a syntax similar to CHARMM's powerful selection commands. MDAnalysis
enables both novice and experienced programmers to rapidly write their
own analytical tools and access data stored in trajectories in an easily
accessible manner that facilitates interactive explorative analysis.
MDAnalysis has been tested on and works for most Unix-based platforms
such as Linux and Mac OS X. It is freely available under the GNU General
Public License from http://mdanalysis.googlecode.com.
authors:
- given-names: "Naveen"
family-names: "Michaud-Agrawal"
- given-names: "Elizabeth J."
family-names: "Denning"
- given-names: "Thomas B."
family-names: "Woolf"
- given-names: "Oliver"
family-names: "Beckstein"
journal: "Journal of Computational Chemistry"
volume: 32
number: 10
pages: "2319-2327"
year: 2011
doi: "10.1002/jcc.21787"
url: "https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.21787"
keywords:
- "molecular dynamics simulations"
- "analysis"
- "proteins"
- "object-oriented design"
- "software"
- "membrane systems"
- "Python programming language"
- type: "software"
title: "pyedr"
abstract: "Reads Gromacs EDR file to populate a pandas dataframe"
authors:
- given-names: "Jonathan"
family-names: "Barnoud"
- given-names: "Manuel Nuno"
family-names: "Melo"
- given-names: "Max"
family-names: "Linke"
- given-names: "Len"
family-names: "Kimms"
alias: "ezavod"
email: "[email protected]"
tel: "+49 251 83-29154"
fax: "+49 251 83-29159"
affiliation: "University of Münster, Institute for Physical Chemistry"
address: "Corrensstraße 28/30"
city: "Münster"
post-code: 48149
country: "DE"
region: "North Rhine-Westphalia"
orcid: "https://orcid.org/0000-0003-2769-923X"
- given-names: "Bjarne"
family-names: "Feddersen"
- given-names: "Oliver"
family-names: "Beckstein"
- given-names: "Hugo"
family-names: "MacDermott-Opeskin"
- given-names: "Irfan"
family-names: "Alibay"
url: "https://github.com/MDAnalysis/panedr"
repository-code: "https://github.com/MDAnalysis/panedr"
license: "LGPL-2.1"
license-url: "https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html"
- type: "software"
title: "NumPy"
abstract: "The fundamental package for scientific computing with Python."
authors:
- name: "All Contributors to NumPy"
url: "https://numpy.org"
repository-code: "https://github.com/numpy/numpy"
license: "BSD-3-Clause"
license-url: "https://opensource.org/licenses/BSD-3-Clause"
keywords:
- "python"
- "numpy"
- "closember"
- type: "article"
title: "Array programming with NumPy"
abstract: >-
Array programming provides a powerful, compact and expressive syntax for
accessing, manipulating and operating on data in vectors, matrices and
higher-dimensional arrays. NumPy is the primary array programming library
for the Python language. It has an essential role in research analysis
pipelines in fields as diverse as physics, chemistry, astronomy,
geoscience, biology, psychology, materials science, engineering, finance
and economics. For example, in astronomy, NumPy was an important part of
the software stack used in the discovery of gravitational waves and in
the first imaging of a black hole. Here we review how a few fundamental
array concepts lead to a simple and powerful programming paradigm for
organizing, exploring and analysing scientific data. NumPy is the
foundation upon which the scientific Python ecosystem is constructed. It
is so pervasive that several projects, targeting audiences with
specialized needs, have developed their own NumPy-like interfaces and
array objects. Owing to its central position in the ecosystem, NumPy
increasingly acts as an interoperability layer between such array
computation libraries and, together with its application programming
interface (API), provides a flexible framework to support the next decade
of scientific and industrial analysis.
authors:
- given-names: "Charles R."
family-names: "Harris"
- given-names: "K. Jarrod"
family-names: "Millman"
- given-names: "Stéfan J."
family-names: "van der Walt"
- given-names: "Ralf"
family-names: "Gommers"
- given-names: "Pauli"
family-names: "Virtanen"
- given-names: "David"
family-names: "Cournapeau"
- given-names: "Eric"
family-names: "Wieser"
- given-names: "Julian"
family-names: "Taylor"
- given-names: "Sebastian"
family-names: "Berg"
- given-names: "Nathaniel J."
family-names: "Smith"
- given-names: "Robert"
family-names: "Kern"
- given-names: "Matti"
family-names: "Picus"
- given-names: "Stephan"
family-names: "Hoyer"
- given-names: "Marten H."
family-names: "van Kerkwijk"
- given-names: "Matthew"
family-names: "Brett"
- given-names: "Allan"
family-names: "Haldane"
- given-names: "Jaime Fernández"
family-names: "del Río"
- given-names: "Mark"
family-names: "Wiebe"
- given-names: "Pearu"
family-names: "Peterson"
- given-names: "Pierre"
family-names: "Gérard-Marchant"
- given-names: "Kevin"
family-names: "Sheppard"
- given-names: "Tyler"
family-names: "Reddy"
- given-names: "Warren"
family-names: "Weckesser"
- given-names: "Hameer"
family-names: "Abbasi"
- given-names: "Christoph"
family-names: "Gohlke"
- given-names: "Travis E."
family-names: "Oliphant"
journal: "Nature"
volume: 585
number: 7825
pages: "357-362"
year: 2020
month: 9
publisher:
name: "Springer Science and Business Media LLC"
doi: "10.1038/s41586-020-2649-2"
url: "https://doi.org/10.1038/s41586-020-2649-2"
- type: "software"
title: "SciPy"
abstract: "Fundamental algorithms for scientific computing in Python"
authors:
- given-names: "Ralf"
family-names: "Gommers"
- given-names: "Pauli"
family-names: "Virtanen"
- given-names: "Evgeni"
family-names: "Burovski"
- given-names: "Warren"
family-names: "Weckesser"
- given-names: "Travis E."
family-names: "Oliphant"
- given-names: "David"
family-names: "Cournapeau"
- given-names: "Matt"
family-names: "Haberland"
- given-names: "Tyler"
family-names: "Reddy"
- given-names: "Pearu"
family-names: "Peterson"
- given-names: "Andrew"
family-names: "Nelson"
- given-names: "Josh"
family-names: "Wilson"
- given-names: "Nikolay"
family-names: "Mayorov"
- given-names: "Ílhan"
family-names: "Polat"
- given-names: "Stéfan J."
family-names: "van der Walt"
- given-names: "Denis"
family-names: "Laxalde"
- given-names: "Matthew"
family-names: "Brett"
- given-names: "Eric"
family-names: "Larson"
- given-names: "Jarrod"
family-names: "Millman"
- given-names: "Pamphile"
family-names: "Roy"
- given-names: "Paul"
family-names: "van Mulbregt"
- given-names: "C J"
family-names: "Carey"
- given-names: "Atsushi"
family-names: "Sakai"
- given-names: "Eric"
family-names: "Moore"
- given-names: "Robert"
family-names: "Kern"
- name: "All Contributors to SciPy"
identifiers:
- description: "The concept DOI of the work."
type: "doi"
value: "10.5281/zenodo.595738"
url: "https://scipy.org"
repository-code: "https://github.com/scipy/scipy"
license: "BSD-3-Clause"
license-url: "https://opensource.org/licenses/BSD-3-Clause"
keywords:
- "python"
- "scipy"
- "algorithms"
- "scientific computing"
- "closember"
- type: "article"
title: >-
SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python
abstract: >-
SciPy is an open-source scientific computing library for the Python
programming language. Since its initial release in 2001, SciPy has become
a de facto standard for leveraging scientific algorithms in Python, with
over 600 unique code contributors, thousands of dependent packages, over
100,000 dependent repositories and millions of downloads per year. In
this work, we provide an overview of the capabilities and development
practices of SciPy 1.0 and highlight some recent technical developments.
authors:
- given-names: "Pauli"
family-names: "Virtanen"
- given-names: "Ralf"
family-names: "Gommers"
- given-names: "Travis E."
family-names: "Oliphant"
- given-names: "Matt"
family-names: "Haberland"
- given-names: "Tyler"
family-names: "Reddy"
- given-names: "David"
family-names: "Cournapeau"
- given-names: "Evgeni"
family-names: "Burovski"
- given-names: "Pearu"
family-names: "Peterson"
- given-names: "Warren"
family-names: "Weckesser"
- given-names: "Jonathan"
family-names: "Bright"
- given-names: "Stéfan J."
family-names: "van der Walt"
- given-names: "Matthew"
family-names: "Brett"
- given-names: "Joshua"
family-names: "Wilson"
- given-names: "K. Jarrod"
family-names: "Millman"
- given-names: "Nikolay"
family-names: "Mayorov"
- given-names: "Andrew R. J."
family-names: "Nelson"
- given-names: "Eric"
family-names: "Jones"
- given-names: "Robert"
family-names: "Kern"
- given-names: "Eric"
family-names: "Larson"
- given-names: "C J"
family-names: "Carey"
- given-names: "Ílhan"
family-names: "Polat"
- given-names: "Yu"
family-names: "Feng"
- given-names: "Eric W."
family-names: "Moore"
- given-names: "Jake"
family-names: "VanderPlas"
- given-names: "Denis"
family-names: "Laxalde"
- given-names: "Josef"
family-names: "Perktold"
- given-names: "Robert"
family-names: "Cimrman"
- given-names: "Ian"
family-names: "Henriksen"
- given-names: "E. A."
family-names: "Quintero"
- given-names: "Charles R."
family-names: "Harris"
- given-names: "Anne M."
family-names: "Archibald"
- given-names: "Antônio H."
family-names: "Ribeiro"
- given-names: "Fabian"
family-names: "Pedregosa"
- given-names: "Paul"
family-names: "van Mulbregt"
- name: "SciPy 1.0 Contributors"
journal: "Nature Methods"
volume: 17
number: 3
pages: "261-272"
year: 2020
publisher:
name: "Nature Publishing Group"
doi: "10.1038/s41592-019-0686-2"
url: "https://rdcu.be/b08Wh"
- type: "software"
title: "matplotlib"
abstract: "Matplotlib: Visualization with Python"
authors:
- given-names: "Thomas A."
family-names: "Caswell"
- given-names: "Michael"
family-names: "Droettboom"
- given-names: "Antony"
family-names: "Lee"
- given-names: "Elliott Sales"
family-names: "de Andrade"
- given-names: "Tim"
family-names: "Hoffmann"
- given-names: "John D."
family-names: "Hunter"
- given-names: "Jody"
family-names: "Klymak"
- given-names: "Eric"
family-names: "Firing"
- given-names: "David"
family-names: "Stansby"
- given-names: "Nelle"
family-names: "Varoquaux"
- given-names: "Jens Hedegaard"
family-names: "Nielsen"
- given-names: "Benjamin"
family-names: "Root"
- given-names: "Ryan"
family-names: "May"
- given-names: "Phil"
family-names: "Elson"
- given-names: "Jouni K."
family-names: "Seppänen"
- given-names: "Darren"
family-names: "Dale"
- given-names: "Jae-Joon"
family-names: "Lee"
- given-names: "Damon"
family-names: "McDougall"
- given-names: "Andrew"
family-names: "Straw"
- given-names: "Paul"
family-names: "Hobson"
- given-names: "Christoph"
family-names: "Gohlke"
- given-names: "Adrien F."
family-names: "Vincent"
- given-names: "Tony S."
family-names: "Yu"
- given-names: "Eric"
family-names: "Ma"
- given-names: "Steven"
family-names: "Silvester"
- given-names: "Charlie"
family-names: "Moad"
- given-names: "Nikita"
family-names: "Kniazev"
- given-names: "Elan"
family-names: "Ernest"
- given-names: "Paul"
family-names: "Ivanov"
- name: "All Contributors to matplotlib"
identifiers:
- description: "The concept DOI of the work."
type: "doi"
value: "10.5281/zenodo.592536"
url: "https://matplotlib.org"
repository-code: "https://github.com/matplotlib/matplotlib"
license: "PSF-2.0"
license-url: "https://matplotlib.org/stable/users/project/license.html"
keywords:
- "python"
- "matplotlib"
- "plotting"
- "tk"
- "gtk"
- "qt"
- "wx"
- "data-science"
- "data-visualization"
- "hacktoberfest"
- type: "article"
title: "Matplotlib: A 2D graphics environment"
abstract: >-
Matplotlib is a 2D graphics package used for Python for application
development, interactive scripting,and publication-quality image
generation across user interfaces and operating systems.
authors:
- given-names: "John D."
family-names: "Hunter"
journal: "Computing in Science & Engineering"
volume: 9
number: 3
pages: "90-95"
year: 2007
publisher:
name: "IEEE COMPUTER SOC"
doi: "10.1109/MCSE.2007.55"
- type: "software"
title: "psutil"
abstract: "Cross-platform lib for process and system monitoring in Python"
authors:
- given-names: "Giampaolo"
family-names: "Rodola"
- name: "All Contributors to psutil"
url: "https://github.com/giampaolo/psutil"
repository-code: "https://github.com/giampaolo/psutil"
license: "BSD-3-Clause"
license-url: "https://opensource.org/licenses/BSD-3-Clause"
keywords:
- "ps"
- "top"
- "kill"
- "free"
- "lsof"
- "netstat"
- "nice"
- "tty"
- "ionice"
- "uptime"
- "taskmgr"
- "process"
- "df"
- "iotop"
- "iostat"
- "ifconfig"
- "taskset"
- "who"
- "pidof"
- "pmap"
- "smem"
- "pstree"
- "monitoring"
- "ulimit"
- "prlimit"
- "performance"
- "metrics"
- "agent"
- "observability"