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Online bioinformatics forums: why do we keep asking the same questions?

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Online bioinformatics forums: why do we keep asking the same questions?

  1. 1. Online bioinformatics forums why do we keep asking the same questions? Neil Saunders Digital Productivity
  2. 2. Forums: Slide 2 of 21 warning: this is not a scientific survey
  3. 3. Forums: Slide 3 of 21 some online forums relevant to bioinformatics
  4. 4. Forums: Slide 4 of 21 Biostars
  5. 5. Forums: Slide 5 of 21 why contribute?
  6. 6. Forums: Slide 6 of 21 there are no stupid questions
  7. 7. Forums: Slide 7 of 21 common questions #1 - “doing things with FASTA files” How To Transform An Interleaved Fasta File To A Sequential Fasta File Change Fasta Id’S Extracting Sequence From A 3Gb Fasta File Fasta sequence of nucleotide sequences How To Save A Mirbase Search Result Into A Fasta File Searching Fasta File For Specific Ids Problem With Fasta Parser Parsing Fasta Headers Using Perl Language Remove Motif Sequence From The Fasta File Of Sequences Mean Length Of Fasta Sequences
  8. 8. Forums: Slide 8 of 21 common questions #2 - “match/compare/intersect” How to compare 2 VCF files Compare Two Fasta Files By Headers Comparing The Numbers Present In Two Files And Get The Matched Intersect Bam Files Plink: Quick Way To Combine Two Datasets Using Only Common Markers Intersect Bam Files intersecting bed and vcf files Tool for finding unique sets of proteins Fast search for many patterns Filter A Tsv File Content Based On Content From Other Tsv Files?
  9. 9. Forums: Slide 9 of 21 common questions #3 - “is my result significant?” Detecting Different Amino Acid Composition Between Two Bacterial Genomes? Is It Important That A Significant Snp Should Be In Ld With It Nearby Snps? Are P-Values Obtained From Two Separate Analyses On The Same Population Comparable? Select significant terms under a parent GO term Significance of overlap between multiple lists Minimum Or Optimal Rpkm Value To Find If A Transcript Is Significant Significant Biology analysis using differentially expressed genes How Many Samples At Least Are Needed To Discover New Snps For Statistical Significance Any Tools To Identify Significantly Altered Pathways? How To Get Significant Genes From Microarray Experiments Data In Geo
  10. 10. Forums: Slide 10 of 21 example questions #4 - “convert ID X to ID Y” this is the one that comes up over and over and over... Convert Uniprot Id To Pdb Id How To Convert Ccds Ids To Swiss Prot Ids How To Convert Arabidopsis Gene Id To Ncbi Geneid, Ncbi-Gi Or Uniprot? How To Convert Refseq Id To Gene Symbol As Pitx1 Converting Protein Names To Gene Ids How To Convert Affymetrix Ids To Genbank Ids How to get list of GeneIDs using SNP ID list? How To Convert Uniprot Ids To Ensemble Gene/Transcript Ids Info Needed Regarding Gene Id Conversion From Agilent To Others Convert kegg ids to uniprot ids
  11. 11. Forums: Slide 11 of 21 Why do the same questions keep coming up?
  12. 12. Forums: Slide 12 of 21 can site design help? - cf. stackoverflow live search, similar posts, autosuggest
  13. 13. Forums: Slide 13 of 21 SEO / Google issues? - apparently not
  14. 14. Forums: Slide 14 of 21 cultural issues: lack of community awareness ? for me, for free, right now
  15. 15. Forums: Slide 15 of 21 cultural issues: “quick fixes over principles” ?
  16. 16. Forums: Slide 16 of 21 better question #1 How To Extract Multiple Fasta Sequences From A File With Perl? How to parse Fasta (and other formats), then perform operations on the parsed elements?
  17. 17. Forums: Slide 17 of 21 better question #2 Matching Ensemble Ids In Input And Library File Using R What are some useful utilities for processing plain-text files?
  18. 18. Forums: Slide 18 of 21 better question #3 Significant Biology analysis using differentially expressed genes What statistical methods are appropriate for the data that I have?
  19. 19. Forums: Slide 19 of 21 better question #4 Convert Official Gene Symbols To Uniprot Ids In Python ? What resources are there to convert between various identifiers?
  20. 20. Forums: Slide 20 of 21 summary are Q & A sites effective resources ? are we helping (can we help?) people ask “better questions” ? are we doing enough to develop “principles of bioinformatic analysis” ?