bioSyntax: 為生物文本上色的plugin

bioSyntax:提供文字編輯器的plugin，幫助生物文本上色，可支援的文本：

• .fasta：一般的核酸或是蛋白質序列
• .fastq：Fasta + Phred score檔案，看序列內容與品質
• .clustal：Multiple Sequence Alignment (MSA)
• .bed：基因體範圍規範檔
• .gtf：基因體註解檔案
• .pdb：蛋白質三級結構
• .vcf：Variant Caller Format，標註基因體上面的變異
• .sam：Sequence Alignment Map (SAM) 次世代定序檔

上面是sublime, vim, gedit, less等文字編輯器可看到～

目前看起來支援性最好的是sublime，延伸支援的格式有：

• .fai：Fasta index
• .flagstat：samtools flag summary
• .cwl：Common Workflow Language (CWL) 標準工作流程語言

下面是僅有vim支援的格式有：

• .nexus：Phylogenetics data
• .pml：PyMOL腳本語言

網站的主體分成：

• Installation：安裝教學
• Manual：操作手冊
• Screenshots：使用的畫面
• Source code：GitHub上面的原始碼
• release：點擊直接下載bioSyntax，但還是要參考安裝手冊

相關資料

• bioSyntax: syntax highlighting for computational biology：bioSyntax開發者寫的論文，發表在BMC Bioinformatics的Software
• GTF2.2: A Gene Annotation Format
• Common Workflow Language
• Phylogenetics: Tree building：建立演化樹的投影片
• Nucleic acid notation：核酸的標準單字元縮寫

_EOF_

Postprocess upscale by: 2, Postprocess upscaler: R-ESRGAN 4x+

Time taken: 10.3 sec. on Apple M2 Pro by Extra

Steps: 20, Sampler: Euler, CFG scale: 7, Seed: 718520801, Size: 1024x512, Model hash: 5765695e8f, Model: Dall-e_3_0.3-v2, Denoising strength: 0.36, Version: v1.6.0-2-g4afaaf8a

Time taken: 17.7 sec. on Apple M2 Pro by img2img

Weary with toil, I haste me to my bed,
The dear repose for limbs with travel tired;
But then begins a journey in my head
To work my mind, when body's work's expired:
For then my thoughts--from far where I abide--
Intend a zealous pilgrimage to thee,
And keep my drooping eyelids open wide,
Looking on darkness which the blind do see:
Save that my soul's imaginary sight
Presents thy shadow to my sightless view,
Which, like a jewel hung in ghastly night,
Makes black night beauteous, and her old face new.
   Lo! thus, by day my limbs, by night my mind,
   For thee, and for myself, no quiet find.

Steps: 20, Sampler: Euler, CFG scale: 7, Seed: 718520801, Size: 512x256, Model hash: 5765695e8f, Model: Dall-e_3_0.3-v2, Version: v1.6.0-2-g4afaaf8a

Time taken: 10.3 sec. on Apple M2 Pro