https://www.badgrammargoodsyntax.com/compbio daily 1.0 2025-01-20 https://www.badgrammargoodsyntax.com/compbio/2025/1/20/compbio-029-it-is-january-2025-and-ai-hallucinations-of-academic-references-is-still-a-huge-problem monthly 0.5 2025-01-20 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/7ae0f1f2-6d42-4efc-b118-a4925b09ddb8/Free_chatGPT.jpg Compbio series - CompBio 029: It is January 2025 and AI hallucinations of academic references is still a huge problem - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/7e51e890-2d34-4158-9b38-f8c9ab93417b/Piad_chatGPT.jpg Compbio series - CompBio 029: It is January 2025 and AI hallucinations of academic references is still a huge problem - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/e1c4c5b4-e471-4d54-a585-54faf5703615/Claude+3.5+sonnet.jpg Compbio series - CompBio 029: It is January 2025 and AI hallucinations of academic references is still a huge problem - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.badgrammargoodsyntax.com/compbio/2023/12/17/compbio-028-python-vs-r-an-endless-war monthly 0.5 2023-12-17 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/d0ba8f1a-380c-4171-a451-981f48724c56/Python_vs_R.png Compbio series - CompBio 028: Python vs R: an endless war - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/e8e294a6-b9a4-4efd-b416-6403b5a1a77f/Old_Man.png.jpeg Compbio series - CompBio 028: Python vs R: an endless war - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.badgrammargoodsyntax.com/compbio/2022/12/18/compbio-027-is-ai-generated-code-is-here-to-replace-computational-biologists monthly 0.5 2022-12-19 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/b470d496-b939-4243-b773-9fd52fd39a4f/IMG_6858.jpeg Compbio series - CompBio 027: Is AI generated code here to replace computational biologists? - Make it stand out A 3D printed mini of a dragon person with wings, primed in grey. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/79c6bb46-b7a1-42c5-9de4-a284bebaa8c4/IMG_1419.jpeg Compbio series - CompBio 027: Is AI generated code here to replace computational biologists? - Make it stand out Image of a greenish dragon person from World of Warcraft and a partly painted base with handwritten hex codes pointed from where I grabbed the colours from. Please note that the Ork Flesh hex code is different in this diagram compared to the code below, but this does not matter for the example code purposes. https://www.badgrammargoodsyntax.com/compbio/2022/12/12/compbio-026-using-the-terminal-at-warp-speed monthly 0.5 2022-12-12 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/e496d56d-2d84-4cdb-8b7a-ea60c9103e2f/01.png Compbio series - Compbio 026: Using the terminal at Warp speed - Make it stand out #list all the file prompt lead to the suggested ls -a command. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/9ca5fb0d-895b-4492-8ce5-05066cef4b08/02.png Compbio series - Compbio 026: Using the terminal at Warp speed - Make it stand out ls -a was entered and files (including hidden files) was listed, as expected. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/eed11436-c991-4070-98d6-bba5b6dc8308/03.png Compbio series - Compbio 026: Using the terminal at Warp speed - Make it stand out #tar g zip the example_file. txt prompt lead to the suggested command “tar -zevf example_file.txt.tar.gz example_file.txt” https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/40dfe49d-cfc3-4efc-ab65-988bb1e7f6d0/04.png Compbio series - Compbio 026: Using the terminal at Warp speed - Make it stand out The above tar -zxcf command was entered and then ls -a was run to see that a compressed version of the file was created and it was. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/2be583b7-7899-4806-9caa-04104c5651ee/05.png Compbio series - Compbio 026: Using the terminal at Warp speed - Make it stand out I used rm to delete the unzipped example file so that after the next command, we could see that an uncompressed version had been created. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/fa43738d-4eae-4dc7-9979-b1c4d25d4e20/06.png Compbio series - Compbio 026: Using the terminal at Warp speed - Make it stand out The above tar -xvzf command was entered and then ls -a was run to see that an uncompressed version of the file was created and it was. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/7b33b6cd-a19b-4dc5-a140-41275339f17e/07.png Compbio series - Compbio 026: Using the terminal at Warp speed - Make it stand out I ran the tar -xvzf command and ls -a to see that the uncompressed version of the file had been created and it had. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/af9cb093-1c52-442a-a50e-154a6a74ec38/08.png Compbio series - Compbio 026: Using the terminal at Warp speed - Make it stand out #count all lines in a file where the third column equals exon prompt lead to the suggestion of awk 'if(§3=="exon" print SO? ' file.txt | wc -I https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/9b5f3ceb-ea29-4b49-89c2-76cae40eb9a7/09.png Compbio series - Compbio 026: Using the terminal at Warp speed - Make it stand out I ran the command awk '{if($3=="exon" ){print $0}}' Patens_318_v3.3.gene_exons.gtf | wc -1 and it gave me an answer of 589994 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/025ef972-2903-4a39-825f-00a09f74b780/10.png Compbio series - Compbio 026: Using the terminal at Warp speed - Make it stand out #count all lines in patens_318_v3.3.gene_exons.gtf where the third column eguals exon prompt lead to the grep -c "exon" Patens_318_V3.3.gene_exons.gtf suggested command. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/c9ae133d-9710-4cdf-bb03-a078b6602e5e/11.png Compbio series - Compbio 026: Using the terminal at Warp speed - Make it stand out grep -c "exon" Ppatens_318_v3.3.gene_exons.gtf command gave the same answer for number of exon lines as before: 589994 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/c71d7711-f2a0-4e13-9916-05d9326bc2a5/12.png Compbio series - Compbio 026: Using the terminal at Warp speed - Make it stand out #Count all lines in Patens_318_v3.3.gene_exons.gtf that contain exon in column 3 and Chr02 in column 1 prompt generated a new command that is so long that it is clipped off (see image description below for command). https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/665a2541-ae51-4c6a-8980-e0fb8c7f8b1c/13.png Compbio series - Compbio 026: Using the terminal at Warp speed - Make it stand out The output of head -20 and the command grep -c "exon" Patens_318_v3.3.gene_exons.gtf | grep "Chr02" from the AI suggestion above. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/7c2309ce-794e-4103-8d75-43a5b174b7a8/14.png Compbio series - Compbio 026: Using the terminal at Warp speed - Make it stand out grep -c "exon" Ppatens_318_V3.3.gene_exons.gtf | grep "Chr02" gave an error, as expected, meanwhile grep "exon" patens_318 _v3.3.gene_exons.gtf | grep -c "Chr02” gave and answer of 34480 https://www.badgrammargoodsyntax.com/compbio/2022/9/27/compbio-024-git-for-digital-dummies-and-why-version-control-matters monthly 0.5 2024-01-11 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1b12f075-25fe-4aff-b44e-8b5568db1842/git.jpg Compbio series - Compbio 025: Git for digital noobs (and why version control matters) - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/2ed565f1-b2a2-4f7f-8bfd-ac9310c3aeb2/IMG_1189.jpeg Compbio series - Compbio 025: Git for digital noobs (and why version control matters) - Make it stand out Details of how to save changes in a file to a git repo. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/468fcc82-0c7b-47d6-99b0-f9ace6b04429/IMG_1190.jpeg Compbio series - Compbio 025: Git for digital noobs (and why version control matters) - Make it stand out Diagram of how git branches work, with cartoon bunnies. https://www.badgrammargoodsyntax.com/compbio/2022/9/28/compbio-024-a-bioinformagician monthly 0.5 2022-09-28 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/d48291fa-f5fc-4d80-8271-a76dabb95479/IMG_1198.jpeg Compbio series - Compbio 024: A Bioinformagician - Make it stand out Entrance to the mines of Moria asking in Elvish to “Speak Friend and Enter” and then pseudo-code for opening a door if friend in elvish is spoken. https://www.badgrammargoodsyntax.com/compbio/2020/8/2/compbio-023-use-screen-to-prevent-compute-server-disconnect monthly 0.5 2020-08-02 https://www.badgrammargoodsyntax.com/compbio/2018/12/31/compbio-022-differential-splicing-and-transcripts-not-as-simple-as-it-first-appears monthly 0.5 2019-01-02 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1546220317582-R09TS3DSWVDNADNQ3M1S/Figure1-01.png Compbio series - Compbio 022: Differential splicing and transcripts - Not as simple as it first appears Figure 1 - Blue boxes are constitutive exons , orange is an alternative (skipped) exon. Brown boxes are short reads from RNA-seq. Lines represent splice junctions (locations of intron removal). https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1546220410869-BT0WXP60VH2EVDM2ESHF/Figure2-01.png Compbio series - Compbio 022: Differential splicing and transcripts - Not as simple as it first appears Figure 2 - A third isoform is introduced compared to Figure 1. Lack of reads supporting it suggest that it might be an artefact in the annotation. https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1546220485955-YG1K91XD83B2BSBHHTFX/Figure3-01.png Compbio series - Compbio 022: Differential splicing and transcripts - Not as simple as it first appears Figure 3 - Many transcript isoforms can exist per gene. Many events may appear to be co-spliced with distant events. When using standard short read data, it is impossible to know if these events are really co-regulated or if they just appear that way in the annotation, because a single short read cannot link the two together. https://www.badgrammargoodsyntax.com/compbio/2018/3/25/compbio-021-upsets-to-replace-complex-venn-diagrams monthly 0.5 2018-04-02 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1521952056015-ZHOECCY2NY1U0ISMW6HJ/nature11241-f4.2.jpg Compbio series - Compbio 021: UpSetting the status quo - UpSets replace complex Venn diagrams https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1521952116299-7CZ8P1NX6UDK0B38GA83/FantasticBeast1.png Compbio series - Compbio 021: UpSetting the status quo - UpSets replace complex Venn diagrams https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1521952155217-NIKSTJ7OJ91TD9TW2OKP/FantasticBeast2.png Compbio series - Compbio 021: UpSetting the status quo - UpSets replace complex Venn diagrams https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1521952196729-S9XB72CI3FR53P4GHOER/FantasticBeast3.png Compbio series - Compbio 021: UpSetting the status quo - UpSets replace complex Venn diagrams https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1521952236293-BUCZH8GQQIXMLHNTZFTC/FantasticBeast4.png Compbio series - Compbio 021: UpSetting the status quo - UpSets replace complex Venn diagrams https://www.badgrammargoodsyntax.com/compbio/2018/3/5/compbio-020-reads-fragments-and-inserts-what-you-need-to-know-for-understanding-your-sequencing-data-1 monthly 0.5 2018-03-05 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1520254283437-I4YFK7H7EB7HJPCN1K8S/Fig1.jpg Compbio series - Compbio 020: Reads, fragments and inserts - what you need to know for understanding your sequencing data https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1520254378771-9V9Y7HMW9OYXHZVOTRDF/Fig2.jpg Compbio series - Compbio 020: Reads, fragments and inserts - what you need to know for understanding your sequencing data https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1520254339743-LYLF8FRUGR0IZ083YUHX/Fig3.jpg Compbio series - Compbio 020: Reads, fragments and inserts - what you need to know for understanding your sequencing data https://www.badgrammargoodsyntax.com/compbio/2018/1/14/compbio-019-getting-the-most-out-of-your-data-on-the-command-line monthly 0.5 2018-01-21 https://www.badgrammargoodsyntax.com/compbio/2018/1/8/compbio-018-getting-more-significance-out-of-r monthly 0.5 2018-01-08 https://www.badgrammargoodsyntax.com/compbio/2017/12/16/compbio-017-is-your-overlap-significant monthly 0.5 2017-12-26 https://www.badgrammargoodsyntax.com/compbio/2017/12/16/compbio-016-practical-python-for-biologists-moving-from-python2-to-python3 monthly 0.5 2017-12-19 https://www.badgrammargoodsyntax.com/compbio/2017/12/9/compbio-015-practical-python-for-biologists-processing-two-input-files monthly 0.5 2017-12-10 https://www.badgrammargoodsyntax.com/compbio/2017/12/3/compbio-014-practical-python-for-biologists-finding-motifs-with-python monthly 0.5 2017-12-04 https://www.badgrammargoodsyntax.com/compbio/2017/11/26/compbio-013-practical-python-for-biologists-opening-and-saving-files monthly 0.5 2017-11-27 https://www.badgrammargoodsyntax.com/compbio/2017/10/29/compbio-012-making-venn-diagrams-the-right-way-using-python monthly 0.5 2020-01-02 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1509270172131-J5T6WKTIPDRJKT9MMXK1/01_two-way_no_title.png Compbio series - Compbio 012: Making Venn diagrams the right way (using Python) https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1509270506632-T8VV3N64QER3YTFZ1M3N/02_two-way_title.png Compbio series - Compbio 012: Making Venn diagrams the right way (using Python) https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1509270630543-OWSTIMN7YBDL72E66U09/03_three-way_large_overlap.png Compbio series - Compbio 012: Making Venn diagrams the right way (using Python) https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1509270671930-9EPPLDEMR7HE0EDZB68O/04_three-way_small_overlap.png Compbio series - Compbio 012: Making Venn diagrams the right way (using Python) https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1509270712871-YGQ6DJSEJHL53RV2SC0A/05_three-way_uneven_samples.png Compbio series - Compbio 012: Making Venn diagrams the right way (using Python) https://www.badgrammargoodsyntax.com/compbio/2017/10/29/compbio-011-the-fantastic-jupyter-ipython-notebook monthly 0.5 2017-11-14 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1509268429572-DKN8YUR8D8F150E62G6N/01_Opening_new_notebook.PNG Compbio series - Compbio 011: The fantastic Jupyter (IPython) notebook https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1510695327099-RCKTIH0FS208P5QYGBTS/new_02.PNG Compbio series - Compbio 011: The fantastic Jupyter (IPython) notebook https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1510695436597-S91YO913KJY84XNUBWBU/new_03.PNG Compbio series - Compbio 011: The fantastic Jupyter (IPython) notebook https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1509268575595-H2QFKBRWJGC24BOJ604K/04_Markdown.PNG Compbio series - Compbio 011: The fantastic Jupyter (IPython) notebook https://www.badgrammargoodsyntax.com/compbio/2017/10/28/compbio-009-ubuntu-on-windows monthly 0.5 2018-08-10 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1509194187251-XY8G9MK0RBZQ4I373QXP/01_App_store.PNG Compbio series - Compbio 010: Ubuntu on Windows https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1509194270854-QXPIVB7YZ8944Z5HGOET/02_Needs_enabling.PNG Compbio series - Compbio 010: Ubuntu on Windows https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1509194481475-QRON1R1M55WGSOYC4LQ2/04_Enabling_part_2.PNG Compbio series - Compbio 010: Ubuntu on Windows https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1509194520369-WN9H6A81YIB502LYZWWN/05_Enabling_part_3-Restart.PNG Compbio series - Compbio 010: Ubuntu on Windows https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1509194589639-LP8O1P4OJ2RN1IK9O7AJ/image-asset.png Compbio series - Compbio 010: Ubuntu on Windows https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1509194732967-JEMINVQH8K7FOAIFSHNF/09_Version_check.PNG Compbio series - Compbio 010: Ubuntu on Windows https://www.badgrammargoodsyntax.com/compbio/2017/10/28/009-practical-python-for-biologists-what-are-modules monthly 0.5 2019-09-08 https://www.badgrammargoodsyntax.com/compbio/2017/10/26/compbio-008-what-the-fastq-file-formats-in-compbio monthly 0.5 2018-01-13 https://www.badgrammargoodsyntax.com/compbio/2017/10/15/compbio-007-a-better-way-to-show-your-data-with-r-an-end-to-bar-plots monthly 0.5 2017-10-23 https://images.squarespace-cdn.com/content/v1/59a1d86e6a49631dd51560f2/1508065006301-H5C3974T6VL8NTIAY3A2/Bar_plot.png Compbio series - 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