Common Knowledge

OA and H1N1 Influenza

Quick hit at the end of the week. I’ve got a couple of posts I’m trying to finish up and post next week.

But it’s worth noting that the new H1N1 is sequenced and available under the same open access terms as the rest of the NCBI data and contents.

All that misery and expense and illness, from this short series of letters. Nature’s one hell of a programmer.

1 atggatgtca atccgactct acttttccta aaaattccag cgcaaaatgc cataagcacc
61 acattccctt atactggaga tcctccatac agccatggaa caggaacagg atacaccatg
121 gacacagtaa acagaacaca ccaatactca gaaaagggaa agtggacgac aaacacagag
181 actggtgcac cccagctcaa cccgattgat ggaccactac ctgaggataa tgaaccaagt
241 gggtatgcac aaacagactg tgttctagag gctatggctt tccttgaaga atcccaccca
301 ggaatatttg agaattcatg ccttgaaaca atggaagttg ttcaacaaac aagggtagat
361 aaactaactc aaggtcgcca gacttatgat tggacattaa acagaaatca accggcagca
421 actgcattgg ccaacaccat agaagtcttc agatcgaatg gcctaacagc taatgagtca
481 ggaaggctaa tagatttctt aaaggatgta atggaatcaa tgaacaaaga ggaaatagag
541 ataacaaccc actttcaaag aaaaaggaga gtaagagaca acatgaccaa gaagatggtc
601 acgcaaagaa caatagggaa gaaaaaacaa agactgaata agagaggcta tctaataaga
661 gcactgacat taaatacgat gaccaaagat gcagagagag gcaagttaaa aagaagggct
721 atcgcaacac ctgggatgca gattagaggt ttcgtatact ttgttgaaac tttagctagg
781 agcatttgcg aaaagcttga acagtctggg ctcccagtag ggggcaatga aaagaaggcc
841 aaactggcaa atgttgtgag aaagatgatg actaattcac aagacacaga gatttctttc
901 acaatcactg gggacaacac taagtggaat gaaaatcaaa atcctcgaat gttcctggcg
961 atgattacat atatcaccag aaatcaaccc gagtggttca gaaacatcct gagcatggca
1021 cccataatgt tctcaaacaa aatggcaaga ctagggaaag ggtacatgtt cgagagtaaa
1081 agaatgaaga ttcgaacaca aataccagca gaaatgctag caagcattga cctgaagtac
1141 ttcaatgaat caacaaagaa gaaaattgag aaaataaggc ctcttctaat agatggcaca
1201 gcatcactga gtcctgggat gatgatgggc atgttcaaca tgctaagtac ggtcttggga
1261 gtctcgatac tgaatcttgg acaaaagaaa tacaccaaga caatatactg gtgggatggg
1321 ctccaatcat ccgacgattt tgctctcata gtgaatgcac caaaccatga gggaatacaa
1381 gcaggagtgg acagattcta caggacctgc aagttagtgg gaatcaacat gagcaaaaag
1441 aagtcctata taaataagac agggacattt gaattcacaa gcttttttta tcgctatgga
1501 tttgtggcta attttagcat ggagctaccc agctttggag tgtctggagt aaatgaatca
1561 gctgacatga gtattggagt aacagtgata aagaacaaca tgataaacaa tgaccttgga
1621 cctgcaacgg cccagatggc tcttcaattg ttcatcaaag actacagata cacatatagg
1681 tgccataggg gagacacaca aattcagacg agaagatcat ttgagttaaa gaagctgtgg
1741 gatcaaaccc aatcaaaggt agggctatta gtatcagatg gaggaccaaa cttatacaat
1801 atacggaatc ttcacattcc tgaagtctgc ttaaaatggg agctaatgga tgatgattat
1861 cggggaagac tttgtaatcc cctgaatccc tttgtcagtc ataaagagat tgattctgta
1921 aacaatgctg tggtaatgcc agcccatggt ccagccaaaa gcatggaata tgatgccgtt
1981 gcaactacac attcctggat tcccaagagg aatcgttcta ttctcaacac aagccaaagg
2041 ggaattcttg aggatgaaca gatgtaccag aagtgctgca atctattcga gaaatttttc
2101 cctagcagtt catataggag accggttgga atttctagca tggtggaggc catggtgtct
2161 agggcccgga ttgatgccag ggtcgacttc gagtctggac ggatcaagaa agaagagttc
2221 tctgagatca tgaagatctg ttccaccatt gaagaactca gacggcaaaa ataa

Comments

  1. #1 Steven Salzberg
    May 1, 2009

    Not quite. The Mexican sequences are not in GenBank. The CDC deposited them in GISAID instead – in a database called EpiFluDB, which is free but only to scientists with an account (which includes me). The data are not freely available – you have to agree to restrictions in order to use them. GISAID was originally intended to be a conduit to GenBank – a brief “holding tank” for those scientists who wouldn’t otherwise share their data immediately. But then last fall, GISAID changed its rules, and now they no longer require contributors to release data to GenBank.

    But in this case the Mexican sequences are virtually identical to the other strains (from the U.S. and elsewhere), so it doesn’t really matter that they are not available.

  2. #2 john wilbanks
    May 1, 2009

    Steven – that’s an extremely good point, and I’m red-faced for not noticing it. And I did not know about the GISAID change. I actually signed the original letter and I’m going to look into this – as a signatory to the letter I’d expect to have been informed. Maybe I was. But I don’t remember it.

  3. #3 Steven Salzberg
    May 2, 2009

    John – I was a signatory too. I learned just recently that back in August, the GISAID board had a meeting and changed the policy. The minutes of their meeting are available from the GISAID website, and here’s the relevant part:

    “6. Timing for the release of data to the International Nucleotide Sequence. The Council discusses whether GISAID could or should regulate when a submitter’s sequences would be released to the public domain databases such as the INSDC Collaboration that comprises EMBL/DDBJ/GenBank. Currently the EpiFluDB provides an automated functionality that can move data at the submitter’s request to EMBL/DDBJ/GenBank;

    Citing the varying sensitivities of countries that participate in the GISAID Initiative, the Council reaches a consensus to recommend that such decisions be left in the hands of the individual submitter, to decide when data will be released to EMBL/DDBJ/GenBank.”

    They didn’t notify me either.

  4. #4 resimler
    May 9, 2009

    1
    Not quite. The Mexican sequences are not in GenBank. The CDC deposited them in GISAID instead – in a database called EpiFluDB, which is free but only to scientists with an account (which includes me). The data are not freely available – you have to agree to restrictions in order to use them. GISAID was originally intended to be a conduit to GenBank – a brief “holding tank” for those scientists who wouldn’t otherwise share their data immediately. But then last fall, GISAID changed its rules, and now they no longer require contributors to release data to GenBank.

  5. #5 Lilian Nattel
    May 11, 2009

    I don’t know anything about the proprietary rights, but looking at that sequence of letters is wild. Thinking that I live in a time where it can be written out like that.

  6. #6 parça kontör
    May 15, 2009

    This is off topic but I couldnt load the contact webpage. I am responding to this statement in your bio:

    “Afarensis is currently considered to be transitional between apes and humans and displays some traits of both.”

    Arent humans apes? That statement appears to dichotomize the two.

    Respectfully,

    AN

  7. #7 sevismek
    May 16, 2009

    Steven – that’s an extremely good point, and I’m red-faced for not noticing it. And I did not know about the GISAID change. I actually signed the original letter and I’m going to look into this – as a signatory to the letter I’d expect to have been informed. Maybe I was. But I don’t remember it.

  8. #8 sevişme
    May 21, 2009

    Sam, the question is how do you know that any one commenter is a certain nationality? With the double “aa” in his name tumaat could just as well be Dutch. Declaring all the persons in the third largest country by population with one single attribute is not very bright either.

  9. #9 sevişme
    May 21, 2009

    They also sound like people who are in no condition to be credible credit risks.

    In principle I would agree with this statement. The problem is that for most of the last ten years the banks did not agree. They were eager to get people signed up for the debt treadmill precisely because the interest rates and fees were so profitable for the banks. They never considered what would happen when a large fraction of their borrowers became unable to roll over their debt (the ability of so many borrowers to temporarily cover the credit card bills from the HELOC ATM helped postpone this day of reckoning).