Embed Size (px)
Citation preview
Online bioinformatics forumswhy do we keep asking the same questions?
Neil Saunders
Digital Productivitywww.csiro.au
Forums: Slide 2 of 21
warning: this is not a scientific survey
Forums: Slide 3 of 21
some online forums relevant to bioinformatics
Forums: Slide 5 of 21
why contribute?
Forums: Slide 6 of 21
there are no stupid questions
http://designyoutrust.com/2013/04/33-sick-stupid-questions-from-clients/
Forums: Slide 7 of 21
common questions #1 - “doing things with FASTA files”
How To Transform An Interleaved Fasta File To A Sequential Fasta FileChange Fasta Id’SExtracting Sequence From A 3Gb Fasta FileFasta sequence of nucleotide sequencesHow To Save A Mirbase Search Result Into A Fasta FileSearching Fasta File For Specific IdsProblem With Fasta ParserParsing Fasta Headers Using Perl LanguageRemove Motif Sequence From The Fasta File Of SequencesMean Length Of Fasta Sequences
Forums: Slide 8 of 21
common questions #2 - “match/compare/intersect”
How to compare 2 VCF filesCompare Two Fasta Files By HeadersComparing The Numbers Present In Two Files And Get The MatchedIntersect Bam FilesPlink: Quick Way To Combine Two Datasets Using Only Common MarkersIntersect Bam Filesintersecting bed and vcf filesTool for finding unique sets of proteinsFast search for many patternsFilter A Tsv File Content Based On Content From Other Tsv Files?
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 PopulationComparable?Select significant terms under a parent GO termSignificance of overlap between multiple listsMinimum Or Optimal Rpkm Value To Find If A Transcript Is SignificantSignificant Biology analysis using differentially expressed genesHow Many Samples At Least Are Needed To Discover New Snps For StatisticalSignificanceAny Tools To Identify Significantly Altered Pathways?How To Get Significant Genes From Microarray Experiments Data In Geo
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 IdHow To Convert Ccds Ids To Swiss Prot IdsHow To Convert Arabidopsis Gene Id To Ncbi Geneid, Ncbi-Gi Or Uniprot?How To Convert Refseq Id To Gene Symbol As Pitx1Converting Protein Names To Gene IdsHow To Convert Affymetrix Ids To Genbank IdsHow to get list of GeneIDs using SNP ID list?How To Convert Uniprot Ids To Ensemble Gene/Transcript IdsInfo Needed Regarding Gene Id Conversion From Agilent To OthersConvert kegg ids to uniprot ids
Forums: Slide 11 of 21
Why do the same questions keep coming up?
http://www.googlepoetics.com/
Forums: Slide 12 of 21
can site design help? - cf. stackoverflow
live search, similar posts, autosuggest
Forums: Slide 13 of 21
SEO / Google issues? - apparently not
Forums: Slide 14 of 21
cultural issues: lack of community awareness ?
for me, for free, right now
Forums: Slide 15 of 21
cultural issues: “quick fixes over principles” ?
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?
Forums: Slide 17 of 21
better question #2
Matching Ensemble Ids In Input And Library File Using RWhat are some useful utilities for processing plain-text files?
Forums: Slide 18 of 21
better question #3
Significant Biology analysis using differentially expressed genesWhat statistical methods are appropriate for the data that I have?
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?
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” ?
