Love, Sex and Mushrooms: Adventures of a Woman in Science

[Reposted from FGSC news]

Cardy Raper, University of Vermont Professor Emerita, Microbiology and Molecular Genetics, has just published a memoir titled “Love, Sex and Mushrooms: Adventures of a Woman in Science” (ISBN 978-0-615-43440-7). As Peter R. Day, coauthor of “Plant-Fungal Pathogen Interaction” remarked: “Books about sex in fungi rarely reward the casual interest of the general reader generated by ‘sex’ in their titles….Cardy Raper’s autobiography is a refreshing exception….What makes it so readable and engrossing is her frank account of her circumstances both in and out of the laboratory. This book will encourage aspiring students, men as well as women, in how to overcome difficulties.” And Lorna Casselton, FRS, commented: “Cardy Raper succeeded in being what she dreamed of as a young girl, a successful scientist with her own laboratory. But it was not a conventional path to success….This is the personal story of an exceptional woman scientist.”

Copies of the book will be available at this year’s Fungal Genetics Conference at Asilomar, in March. 

 

The roundup of twittered updates for 2011-02-28

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Neurospora annotation update (v5)

Here is a message from the Broad Institute about a gene annotation update that was made recently in response to an issue that was revealed in the June 2010 release.  This new version is called V5 and should be on its way to GenBank.

Dear Neurospora scientists,

Recently we discovered an issue with the way locus tags were assigned
to our most recent Neurospora gene set, released publicly on the Broad
website in June of 2010. Many genes in this gene set have mismatched
locus numbers compared to the same genes released in February 2010.
Adding to the confusion, both releases were labeled version 4.

To remedy this we have recalled the June locus numbers and released a
new, version 5 gene set. Genes in this set have been numbered to
preserve historical locus numbers (back to the original genbank
release) as much as possible.

Folks who call their favorite genes by their v1, v2 or v3 numbers can
search for them on our web page, which will map them to v5
automatically and accurately. The same will work for most v4 numbers.
Unfortunately, 863 genes have different locus tags in the two v4
releases. If you search for one of them, you will get two hits - the
v5 gene that the February edition mapped to, and the v5 gene that the
June edition mapped to.

Two examples to clarify:

A. Suppose you search for NCU11713.4 on our web page. This query will
retrieve two genes, NCU11688.5 and NCU11713.5. The gene which in the
February release was called NCU11713.4 is the same as NCU11688.5,
while the gene labeled NCU11713.4 in June is the same as NCU11713.5.

B. Searching for NCU11324.4 yields but one hit because that gene, like
most genes, was consistently numbered between the two releases labeled
4.

If you are not sure when you downloaded your genes, the following may
help. If you see any of these locus numbers in your gene set:

NCU00129.4, NCU00457.4, NCU00499.4, NCU00556.4, NCU00627.4,
NCU00685.4, NCU00768.4, NCU00856.4, NCU00986.4, NCU01064.4,
NCU01065.4, NCU01282.4, NCU01299.4, NCU01300.4, NCU01483.4,
NCU01559.4, NCU01560.4, NCU01610.4, NCU01611.4, NCU01664.4,
NCU01665.4, NCU01871.4, NCU01903.4, NCU02200.4, NCU02259.4,
NCU02666.4, NCU02758.4, NCU02837.4, NCU02998.4, NCU03047.4,
NCU03206.4, NCU03773.4, NCU04239.4, NCU04240.4, NCU04518.4,
NCU04519.4, NCU04710.4, NCU04711.4, NCU05275.4, NCU05512.4,
NCU05776.4, NCU06013.4, NCU06370.4, NCU06732.4, NCU07107.4,
NCU07259.4, NCU07260.4, NCU07301.4, NCU07405.4, NCU07856.4,
NCU07857.4, NCU08090.4, NCU08182.4, NCU08323.4, NCU08332.4,
NCU09085.4, NCU09256.4, NCU09257.4, NCU09998.4, NCU10166.4,
NCU10574.4, NCU11040.4, NCU11240.4, NCU11253.4, NCU11376.4,
NCU11390.4, NCU11393.4

then your genes are from the February 2010 gene set. However, if you see

NCU00082.4, NCU00083.4, NCU00084.4, NCU00085.4, NCU00516.4,
NCU01819.4, NCU04299.4, NCU04300.4, NCU04301.4, NCU04302.4,
NCU04303.4, NCU04304.4, NCU04305.4, NCU05000.4, NCU05111.4,
NCU05112.4, NCU05113.4, NCU05114.4, NCU05115.4, NCU05116.4,
NCU05448.4, NCU05452.4, NCU06667.4, NCU07323.4, NCU09066.4,
NCU10179.4, NCU10301.4, NCU10379.4, NCU10383.4, NCU10753.4,
NCU10866.4, NCU10914.4, NCU11068.4, NCU11182.4, NCU12157.4,
NCU12158.4, NCU12159.4, NCU12160.4, NCU12161.4, NCU12162.4,
NCU12163.4, NCU12164.4, NCU12165.4, NCU12166.4, NCU12167.4,
NCU12168.4, NCU12169.4, NCU12170.4, NCU12171.4, NCU12172.4,
NCU12173.4, NCU12174.4, NCU12175.4, NCU12176.4, NCU12177.4,
NCU12178.4, NCU12179.4, NCU12180.4, NCU12181.4, NCU12182.4,
NCU12183.4, NCU12184.4, NCU12185.4, NCU12186.4, NCU12187.4, NCU12188.4

then your genes are from the June 2010 release.

Attached please find five mapping tables which can be used to migrate
locus numbers from any of the previous releases to the latest version
5 locus tags (linked below).

We apologize for any confusion this may cause.
Love,
The Broad Institute

I’ve also uploaded the locus update files which maps between versions of the annotation.

EMBO Conference: Comparative Genomics Of Eukaryotic Microorganisms 2011

Announcing an upcoming conference in October.
Comparative Genomics Of Eukaryotic Microorganisms: Understanding The Complexity Of Diversity

It will be held in Sant Feliux, Spain October  15-20, 2011. The website has more details including an impressive slate of speakers.

I can attest to it being a great meeting from my attendance 2 years ago. A great venue and excellent speakers and plenty of time to linger and discuss ideas and research over meals and coffee breaks.

 

A HyphalTip: Get a bunch of SRA data

[Trying to post some simple tips from time-to-time, they’ll be in this same category]

For those wanting to get a large dataset from NCBI SRA trace archive, you may be annoyed to click on each link and wait for the download. For example if you read a recent paper on Population Genomics in Neurospora crassa and saw the 48 RNA-Seq datasets which is accession number SRP004848, you might be interested to download all these data for your own re-analysis, as a great dataset for teaching, or even to see how the splicing and expression looks for your favorite gene.

I put together some scripts in this folder to make it easy to see how to download, rename, and extract fastq from these data.  In a future HyphalTip, I’ll detail how you can map these to the genome to get expression values and improve gene annotation.

For cmdline users, after installing the aspera plugin, you can do this to download the sra light data.  Aspera will give you 10-100x speedup – I was downloading at 300 MB/s vs 5Mb/s with wget or ncftp (FTP download). See Morgan’s info about downloading as well. You can run this command or see it in this script.

hyphaltip $ ~/.aspera/connect/bin/ascp -k 1 -l 300M -QTr -i ~/.aspera/connect/etc/asperaweb_id_dsa.putty \
anonftp@ftp-private.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByStudy/litesra/SRP/SRP004/SRP004848 ./

Now the IDs you will have for all these files will be for the SRA accessions not the original strain numbers which may be more informative/meaningful. This can be confusing because the accession for a particular experiment is SRR080688 is the strain D110/FGSC 8870. You can get the list of the trace accession and the strain IDs in this link. Sadly there isn’t 1 place to get the SRR accession to strain name, but if you download the brief listing and then the FTP listing (as text) you can map from each ID to the other and make this file with a little bit of Perl-Fu. You can then run this renaming script which will help you rename the files using the remapping file.

Finally to convert these to fastq you can run this dump_fastq.sh script which will dump out fastq files suitable for use in the future steps. These files are all single-end RNA-Seq but if it had been paired end, a _1.fastq and _2.fastq file would have been made for every SRA file (plus a .fastq one for reads that failed in someway).

cd SRP004848
rmdir SRR*
for file in *.lite.sra
do 
  base=`basename $file .lite.sra` 
  fastq-dump -alt 1 -A $base $file
done

Together this is a pretty automated way to get the data you want, once you’ve figured out which accessions you need and how you want to rename them.