-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathindex.html
More file actions
1714 lines (1554 loc) · 55 KB
/
index.html
File metadata and controls
1714 lines (1554 loc) · 55 KB
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
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<!DOCTYPE html>
<html lang="zh-CN">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Bio Studio | AI 生物计算工作台</title>
<meta
name="description"
content="Bio Studio 是一个为 AI agent 组织的生物计算工作台：协议、技能、MCP 服务、隔离项目、共享数据和重型外部引擎共同组成一套可执行研究环境。"
>
<style>
:root {
--bg: #f4efe6;
--bg-strong: #ece4d6;
--surface: #fbf8f3;
--surface-2: #f6f1e8;
--ink: #181411;
--muted: #655c54;
--line: rgba(24, 20, 17, 0.14);
--line-strong: rgba(24, 20, 17, 0.24);
--accent: #9c3d24;
--accent-soft: rgba(156, 61, 36, 0.12);
--teal: #1d5b63;
--teal-soft: rgba(29, 91, 99, 0.12);
--olive: #556247;
--olive-soft: rgba(85, 98, 71, 0.12);
--gold: #ad7a1f;
--gold-soft: rgba(173, 122, 31, 0.14);
--shadow: 0 16px 40px rgba(41, 30, 22, 0.08);
--radius: 12px;
--radius-sm: 8px;
--content: 1380px;
}
* {
box-sizing: border-box;
}
html {
scroll-behavior: smooth;
}
body {
margin: 0;
color: var(--ink);
background:
radial-gradient(circle at top right, rgba(29, 91, 99, 0.12), transparent 28%),
radial-gradient(circle at left center, rgba(156, 61, 36, 0.10), transparent 24%),
linear-gradient(var(--bg), var(--bg));
font-family: "IBM Plex Sans", "Noto Sans SC", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei", sans-serif;
line-height: 1.55;
min-height: 100vh;
}
body::before {
content: "";
position: fixed;
inset: 0;
pointer-events: none;
background-image:
linear-gradient(rgba(24, 20, 17, 0.03) 1px, transparent 1px),
linear-gradient(90deg, rgba(24, 20, 17, 0.03) 1px, transparent 1px);
background-size: 32px 32px;
mask-image: linear-gradient(to bottom, rgba(0, 0, 0, 0.55), transparent 92%);
}
a {
color: inherit;
text-decoration: none;
}
.shell {
width: min(calc(100% - 32px), var(--content));
margin: 0 auto;
padding: 20px 0 72px;
position: relative;
}
.topbar {
display: flex;
align-items: center;
justify-content: space-between;
gap: 18px;
padding: 10px 0 22px;
border-bottom: 1px solid var(--line);
margin-bottom: 28px;
position: sticky;
top: 0;
z-index: 10;
backdrop-filter: blur(14px);
background: rgba(244, 239, 230, 0.86);
}
.brand {
display: flex;
align-items: center;
gap: 12px;
min-width: 0;
}
.brand-mark {
width: 36px;
height: 36px;
border-radius: 10px;
background: var(--ink);
color: var(--bg);
display: grid;
place-items: center;
font-size: 16px;
font-weight: 700;
letter-spacing: 0.03em;
}
.brand-copy {
min-width: 0;
}
.brand-copy strong {
display: block;
font-size: 14px;
font-weight: 700;
}
.brand-copy span {
display: block;
font-size: 12px;
color: var(--muted);
white-space: nowrap;
overflow: hidden;
text-overflow: ellipsis;
}
.topnav {
display: flex;
flex-wrap: wrap;
justify-content: flex-end;
gap: 8px;
}
.topnav a {
border: 1px solid transparent;
border-radius: 999px;
padding: 8px 12px;
font-size: 13px;
color: var(--muted);
transition: background-color 140ms ease, border-color 140ms ease, color 140ms ease;
}
.topnav a:hover,
.topnav a.active {
color: var(--ink);
border-color: var(--line);
background: rgba(255, 255, 255, 0.52);
}
.masthead {
display: grid;
grid-template-columns: 1.2fr 0.8fr;
gap: 22px;
margin-bottom: 22px;
}
.panel {
background: rgba(251, 248, 243, 0.78);
border: 1px solid var(--line);
border-radius: var(--radius);
box-shadow: var(--shadow);
}
.hero {
padding: 30px 30px 26px;
position: relative;
overflow: hidden;
}
.hero::after {
content: "";
position: absolute;
right: -64px;
top: -64px;
width: 220px;
height: 220px;
border-radius: 50%;
background: radial-gradient(circle, rgba(29, 91, 99, 0.17), transparent 72%);
pointer-events: none;
}
.eyeline {
display: flex;
flex-wrap: wrap;
gap: 8px;
margin-bottom: 20px;
}
.token {
display: inline-flex;
align-items: center;
gap: 8px;
border: 1px solid var(--line);
border-radius: 999px;
padding: 6px 12px;
font-size: 12px;
color: var(--muted);
background: rgba(255, 255, 255, 0.5);
}
.token strong {
color: var(--ink);
font-weight: 600;
}
.hero h1 {
margin: 0 0 16px;
font-size: clamp(34px, 4vw, 64px);
line-height: 0.98;
letter-spacing: -0.045em;
max-width: 11ch;
}
.hero p {
margin: 0;
max-width: 65ch;
color: #403932;
font-size: 17px;
}
.hero-note {
margin-top: 24px;
padding-top: 18px;
border-top: 1px solid var(--line);
display: grid;
grid-template-columns: repeat(3, 1fr);
gap: 16px;
}
.hero-note div {
min-width: 0;
}
.hero-note strong {
display: block;
margin-bottom: 6px;
font-size: 14px;
}
.hero-note span {
display: block;
color: var(--muted);
font-size: 13px;
}
.overview {
padding: 22px;
display: grid;
grid-template-rows: auto auto 1fr;
gap: 16px;
}
.overview h2,
.section-header h2,
.subsection h3,
.table-card h3,
.callout h3 {
margin: 0;
font-size: 20px;
letter-spacing: -0.03em;
}
.overview p,
.section-header p,
.subsection p,
.callout p {
margin: 0;
color: var(--muted);
}
.signal-grid {
display: grid;
grid-template-columns: repeat(2, minmax(0, 1fr));
gap: 10px;
}
.signal {
padding: 14px;
border-radius: var(--radius-sm);
border: 1px solid var(--line);
background: rgba(255, 255, 255, 0.56);
}
.signal strong {
display: block;
font-size: 26px;
line-height: 1;
letter-spacing: -0.04em;
margin-bottom: 6px;
}
.signal span {
display: block;
font-size: 12px;
color: var(--muted);
}
.legend {
display: grid;
gap: 8px;
font-size: 13px;
}
.legend div {
display: flex;
align-items: center;
justify-content: space-between;
gap: 12px;
}
.legend b {
font-weight: 600;
}
.legend span {
color: var(--muted);
text-align: right;
}
.section {
margin-top: 26px;
}
.section-header {
display: flex;
align-items: end;
justify-content: space-between;
gap: 16px;
margin-bottom: 16px;
}
.section-header .copy {
max-width: 760px;
}
.section-header .kicker {
color: var(--muted);
font-size: 12px;
padding-bottom: 4px;
}
.layer-stack {
display: grid;
grid-template-columns: 1fr;
gap: 12px;
}
.layer {
display: grid;
grid-template-columns: 100px 1fr 320px;
gap: 18px;
padding: 18px;
align-items: start;
border: 1px solid var(--line);
border-radius: var(--radius);
background: rgba(251, 248, 243, 0.72);
box-shadow: var(--shadow);
opacity: 0;
transform: translateY(10px);
transition: opacity 220ms ease, transform 220ms ease;
}
.layer.visible,
.panel.visible,
.subsection.visible,
.table-card.visible,
.callout.visible {
opacity: 1;
transform: translateY(0);
}
.layer-index {
display: grid;
gap: 8px;
align-content: start;
}
.layer-index strong {
font-size: 12px;
color: var(--muted);
font-weight: 600;
}
.layer-index span {
font-size: 40px;
letter-spacing: -0.05em;
line-height: 0.9;
}
.layer-copy h3 {
margin: 0 0 10px;
font-size: 24px;
letter-spacing: -0.04em;
}
.layer-copy p {
margin: 0 0 12px;
color: var(--muted);
}
.chip-row {
display: flex;
flex-wrap: wrap;
gap: 8px;
}
.chip {
border: 1px solid var(--line);
border-radius: 999px;
padding: 5px 10px;
font-size: 12px;
color: var(--ink);
background: rgba(255, 255, 255, 0.55);
}
.layer-meta {
display: grid;
gap: 10px;
padding-left: 18px;
border-left: 1px solid var(--line);
}
.meta-box {
border: 1px solid var(--line);
border-radius: var(--radius-sm);
padding: 12px;
background: rgba(255, 255, 255, 0.48);
}
.meta-box strong {
display: block;
margin-bottom: 6px;
font-size: 13px;
}
.meta-box span,
.meta-box ul {
display: block;
color: var(--muted);
font-size: 13px;
margin: 0;
padding: 0;
list-style: none;
}
.flow-layout {
display: grid;
grid-template-columns: 1.08fr 0.92fr;
gap: 16px;
align-items: start;
}
.subsection,
.table-card,
.callout {
padding: 20px;
border: 1px solid var(--line);
border-radius: var(--radius);
background: rgba(251, 248, 243, 0.75);
box-shadow: var(--shadow);
opacity: 0;
transform: translateY(10px);
transition: opacity 220ms ease, transform 220ms ease;
}
.svg-frame {
border: 1px solid var(--line);
border-radius: var(--radius-sm);
background: linear-gradient(rgba(255, 255, 255, 0.56), rgba(255, 255, 255, 0.4));
padding: 12px;
margin-top: 14px;
}
svg {
max-width: 100%;
height: auto;
display: block;
}
.path-list {
display: grid;
gap: 10px;
margin-top: 16px;
}
.path-list div {
display: grid;
grid-template-columns: 200px 1fr;
gap: 14px;
padding: 12px 0;
border-bottom: 1px solid var(--line);
}
.path-list div:last-child {
border-bottom: none;
padding-bottom: 0;
}
.path-list code,
.command,
.inline-code {
font-family: "IBM Plex Mono", "JetBrains Mono", "SFMono-Regular", "Consolas", monospace;
font-size: 12.5px;
}
.path-list code {
color: var(--accent);
font-weight: 600;
background: var(--accent-soft);
padding: 3px 6px;
border-radius: 6px;
width: fit-content;
}
.bars {
display: grid;
gap: 12px;
margin-top: 16px;
}
.bar {
display: grid;
gap: 6px;
}
.bar-head {
display: flex;
justify-content: space-between;
gap: 12px;
font-size: 13px;
}
.track {
height: 12px;
border-radius: 999px;
background: rgba(24, 20, 17, 0.08);
overflow: hidden;
}
.fill {
height: 100%;
border-radius: inherit;
background: linear-gradient(90deg, var(--ink), var(--accent));
}
.fill.teal {
background: linear-gradient(90deg, var(--teal), #2d7982);
}
.fill.olive {
background: linear-gradient(90deg, var(--olive), #728362);
}
.fill.gold {
background: linear-gradient(90deg, var(--gold), #cb9937);
}
.grid-2 {
display: grid;
grid-template-columns: repeat(2, minmax(0, 1fr));
gap: 16px;
}
.grid-3 {
display: grid;
grid-template-columns: repeat(3, minmax(0, 1fr));
gap: 16px;
}
.project-card {
border: 1px solid var(--line);
border-radius: var(--radius-sm);
padding: 16px;
background: rgba(255, 255, 255, 0.52);
display: grid;
gap: 10px;
}
.project-card header {
display: flex;
justify-content: space-between;
align-items: start;
gap: 12px;
}
.project-card h3 {
margin: 0;
font-size: 17px;
letter-spacing: -0.025em;
}
.size-pill {
border-radius: 999px;
padding: 4px 10px;
font-size: 11px;
white-space: nowrap;
border: 1px solid var(--line);
color: var(--muted);
}
.project-card p,
.project-card li,
.matrix td,
.matrix th,
.debt-card li {
color: var(--muted);
font-size: 13px;
}
.project-card ul,
.debt-card ul {
margin: 0;
padding-left: 18px;
}
.matrix {
width: 100%;
border-collapse: collapse;
margin-top: 14px;
}
.matrix th,
.matrix td {
text-align: left;
padding: 12px 10px;
border-top: 1px solid var(--line);
vertical-align: top;
}
.matrix th {
color: var(--ink);
font-size: 13px;
font-weight: 600;
}
.status {
display: inline-flex;
align-items: center;
gap: 8px;
font-size: 12px;
border-radius: 999px;
padding: 4px 9px;
border: 1px solid var(--line);
background: rgba(255, 255, 255, 0.56);
width: fit-content;
}
.status::before {
content: "";
width: 8px;
height: 8px;
border-radius: 50%;
background: var(--olive);
}
.status.warn::before {
background: var(--gold);
}
.status.risk::before {
background: var(--accent);
}
.debt-grid {
display: grid;
grid-template-columns: repeat(3, minmax(0, 1fr));
gap: 16px;
margin-top: 16px;
}
.debt-card {
border: 1px solid var(--line);
border-radius: var(--radius-sm);
padding: 16px;
background: rgba(255, 255, 255, 0.52);
}
.debt-card h3 {
margin: 0 0 10px;
font-size: 16px;
letter-spacing: -0.02em;
}
.quickstart {
display: grid;
grid-template-columns: 0.95fr 1.05fr;
gap: 16px;
}
.command-block {
margin-top: 16px;
padding: 14px;
border-radius: var(--radius-sm);
background: #1c1815;
color: #ede6db;
overflow-x: auto;
border: 1px solid rgba(255, 255, 255, 0.08);
}
.command-block code {
white-space: pre;
display: block;
font-family: "IBM Plex Mono", "JetBrains Mono", "SFMono-Regular", "Consolas", monospace;
font-size: 12.5px;
line-height: 1.72;
}
.footer {
display: flex;
justify-content: space-between;
gap: 16px;
margin-top: 28px;
padding-top: 18px;
border-top: 1px solid var(--line);
color: var(--muted);
font-size: 13px;
}
.footer strong {
color: var(--ink);
}
.reveal {
opacity: 0;
transform: translateY(10px);
transition: opacity 220ms ease, transform 220ms ease;
}
.reveal.visible {
opacity: 1;
transform: translateY(0);
}
@media (max-width: 1180px) {
.masthead,
.flow-layout,
.quickstart,
.grid-3,
.debt-grid {
grid-template-columns: 1fr;
}
.layer {
grid-template-columns: 80px 1fr;
}
.layer-meta {
grid-column: 1 / -1;
padding-left: 0;
border-left: 0;
border-top: 1px solid var(--line);
padding-top: 14px;
}
.hero-note {
grid-template-columns: 1fr;
}
.grid-2 {
grid-template-columns: 1fr;
}
}
@media (max-width: 820px) {
.shell {
width: min(calc(100% - 20px), var(--content));
}
.topbar {
position: static;
}
.topnav {
justify-content: flex-start;
}
.path-list div {
grid-template-columns: 1fr;
}
.signal-grid {
grid-template-columns: 1fr 1fr;
}
}
@media (max-width: 620px) {
.hero,
.overview,
.subsection,
.table-card,
.callout,
.layer {
padding: 16px;
}
.signal-grid {
grid-template-columns: 1fr;
}
.hero h1 {
max-width: none;
}
}
</style>
</head>
<body>
<div class="shell">
<header class="topbar">
<div class="brand">
<div class="brand-mark">BS</div>
<div class="brand-copy">
<strong>Bio Studio / AI 生物计算工作台</strong>
<span>/home/vimalinx/Projects/bio_studio</span>
</div>
</div>
<nav class="topnav" aria-label="Page sections">
<a href="#overview">总览</a>
<a href="#layers">六层结构</a>
<a href="#flow">AI 回路</a>
<a href="#projects">项目样本</a>
<a href="#matrix">能力矩阵</a>
<a href="#state">现状</a>
<a href="#entry">入口</a>
</nav>
</header>
<section class="masthead reveal" id="overview">
<article class="hero panel">
<div class="eyeline">
<div class="token"><strong>定位</strong> AI-first bio compute workspace</div>
<div class="token"><strong>范式</strong> protocol + skills + projects + engines</div>
<div class="token"><strong>快照</strong> 2026-03-23 local scan</div>
</div>
<h1>这不是一个普通生信仓库。</h1>
<p>
Bio Studio 更像一套专门给 AI agent 使用的生物计算工作台。它把操作协议、Claude
skills、MCP servers、隔离项目目录、共享参考数据，以及 Evo2 / RFdiffusion /
Biomni 这类重型外部引擎，压进同一个可执行研究环境里。人类读 README，AI 读协议后直接干活。
</p>
<div class="hero-note">
<div>
<strong>它真正卖的不是某一个模型</strong>
<span>而是把“环境、流程、工具、任务现场”收束为一个 AI 可操作的研究面板。</span>
</div>
<div>
<strong>核心资产不只是代码</strong>
<span>还包括样例项目、文档规约、经验记录、共享参考和挂载的外部能力。</span>
</div>
<div>
<strong>正确理解方式</strong>
<span>把它当作“AI 研究操作系统”，而不是单一应用或整洁的 SDK 仓库。</span>
</div>
</div>
</article>
<aside class="overview panel">
<div>
<h2>现场信号</h2>
<p>来自当前仓库扫描的几个关键数值。</p>
</div>
<div class="signal-grid">
<div class="signal">
<strong>6</strong>
<span>隔离项目目录</span>
</div>
<div class="signal">
<strong>9</strong>
<span>本地 Claude skills</span>
</div>
<div class="signal">
<strong>3 / 5</strong>
<span>已落地 / 预留 MCP servers</span>
</div>
<div class="signal">
<strong>4</strong>
<span>active 外部引擎仓库</span>
</div>
</div>
<div class="legend">
<div><b>5.9G</b><span>vendored 外部能力：RFdiffusion、Evo2、Biomni、LiteFold</span></div>
<div><b>2.9G</b><span>项目工作区：案例、结果、分析产物和中间文件</span></div>
<div><b>2</b><span>当前外部仓库处于 dirty 状态：RFdiffusion、litefold/source</span></div>
</div>
</aside>
</section>
<section class="section">
<div class="section-header reveal">
<div class="copy">
<div class="kicker">一句话定性</div>
<h2>Bio Studio 的核心价值，在于把 AI 需要的上下文预先编排好了。</h2>
<p>
你不需要从零教 agent 目录规范、工具入口、项目隔离方式、环境验证规则或常见坑。
这些东西已经被写进文档、脚本、skills 和样例项目里，形成了一层可复用的操作语境。
</p>
</div>
</div>
<div class="grid-2">
<article class="callout reveal">
<h3>它不是什么</h3>
<p>不是纯应用，不是纯算法仓库，也不是单一模型的外壳。</p>
<div class="path-list">
<div>
<code>不是一个整洁 SDK</code>
<span>自研代码相对薄，更多是 wrapper、协议、模板和 orchestration glue。</span>
</div>
<div>
<code>不是只给人看的文档库</code>
<span>很多内容明显是给 agent 当工作约束和执行上下文用的。</span>
</div>
<div>
<code>不是单一科研项目</code>
<span>仓库里同时存在环境维护、教学案例、RNA-seq 分析、设计实验和第三方引擎集成。</span>
</div>
</div>
</article>
<article class="callout reveal">
<h3>它更接近什么</h3>
<p>更像一个 AI 生物计算 studio runtime。</p>
<div class="path-list">
<div>
<code>protocol layer</code>
<span>告诉 agent 在部署工具和跑分析时必须遵守的动作顺序。</span>
</div>
<div>
<code>workspace layer</code>
<span>把真实任务放进项目隔离目录，避免环境和产物相互污染。</span>
</div>
<div>
<code>engine layer</code>
<span>通过 vendored repos 和 MCP，让 AI 直接碰到外部模型与数据库。</span>
</div>
</div>
</article>
</div>
</section>
<section class="section" id="layers">
<div class="section-header reveal">
<div class="copy">
<div class="kicker">仓库地图</div>
<h2>六层结构，决定了这个仓库为什么看起来不像“标准项目”。</h2>
<p>
如果把所有目录平铺看，它会显得很散。把它拆成六层后，角色就清晰了：
规则、骨架、接口、任务现场、外挂引擎、共享与遗留。
</p>
</div>
</div>
<div class="layer-stack">
<article class="layer reveal">
<div class="layer-index">
<strong>Layer 01</strong>
<span>01</span>
</div>
<div class="layer-copy">
<h3>操作手册层</h3>
<p>
这层定义 AI 在仓库中如何行动：先读什么、何时验证环境、何时更新日志、如何避免破坏现有工作区。
它是 agent 的行为约束层，也是 Bio Studio 的真正中控台。
</p>
<div class="chip-row">
<span class="chip">README.md</span>
<span class="chip">CLAUDE.md</span>
<span class="chip">docs/AI_ANALYSIS_PROTOCOL.md</span>
<span class="chip">docs/AI_TOOL_PROTOCOL.md</span>
<span class="chip">docs/BEST_PRACTICES.md</span>
</div>
</div>
<div class="layer-meta">
<div class="meta-box">
<strong>作用</strong>
<span>把“怎么工作”写死，避免 agent 每次从零猜测流程。</span>
</div>
<div class="meta-box">
<strong>关键词</strong>
<span>project isolation / validation first / changelog / rollback</span>
</div>
</div>
</article>
<article class="layer reveal">
<div class="layer-index">
<strong>Layer 02</strong>
<span>02</span>
</div>
<div class="layer-copy">
<h3>自研骨架层</h3>
<p>
这里是 Bio Studio 自己写的脚手架：项目模板生成器、环境快照脚本、CLI wrappers，以及一些
design / analysis glue code。它不是厚框架，但足以把本地工具和项目规范捏成一套骨架。
</p>