Calculating time from submission to publication / Degree of burden in submitting a paper

After "404 not found": a database of non-functional resources in the NAR database collection, I've uploaded my second dataset on figshare:
Calculating time from submission to publication / Degree of burden in submitting a paper.

Calculating time from submission to publication / Degree of burden in submitting a paper. Pierre Lindenbaum,  Ryan Delahanty.
figshare.
Retrieved  10:13, Oct 14, 2012 (GMT)
http://dx.doi.org/10.6084/m9.figshare.96403

This dataset was inspired by this post on biostar, initialy asked by Ryan Delahanty: I was wondering if it would be possible to calculate some kind of a metric for the speed-of-publication for each journal. I'm not sure submitted and accepted dates are available for all papers, but I noticed in XML data there are fields like the following:

<PubmedData>
        <History>
            <PubMedPubDate PubStatus="received">
                <Year>2011</Year>
                <Month>11</Month>
                <Day>29</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="accepted">
                <Year>2011</Year>
                <Month>12</Month>
                <Day>20</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
           (...)

In this dataset, the script 'pubmed.sh" downloads the the journals from http://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.pubmedhelptable45/ , the 'eigenfactors' from http://www.eigenfactor.org.

For each journal , It scans pubmed (starting from year=2000) and get the difference between the date[@PubStatus='received'] and the date[@PubStatus='accepted'].

title	issn	eigenfactor	days
"Acta biochimica Polonica"	0001-527X	0.003996	119.770935960591
"Acta biomaterialia"	1742-7061	0.02152	129.682692307692
"Acta biotheoretica"	0001-5342	0.000844	161.897058823529
"Acta cirurgica brasileira / Sociedade Brasileira para Desenvolvimento Pesquisa em Cirurgia"	0102-8650	0.00128	122.038461538462
"Acta cytologica"	0001-5547	0.002305	65.3006134969325
"Acta diabetologica"	0940-5429	0.001851	299.6
"Acta haematologica"	0001-5792	0.002825	118.654676258993
"Acta histochemica"	0065-1281	0.002162	110.471204188482
"Acta histochemica et cytochemica"	0044-5991	0.000677	81.6455696202532
"Acta neurochirurgica"	0001-6268	0.009685	204.371830985916
"Acta neuropathologica"	0001-6322	0.023471	69.7277882797732
"Acta theriologica"	0001-7051	0.000901	147.0
"Acta tropica"	0001-706X	0.01011	196.577777777778
"Acta veterinaria Scandinavica"	0044-605X	0.001612	82.0
"Addictive behaviors"	0306-4603	0.017915	163.049731182796
"Advances in space research "	0273-1177	0.021217	205.0
Ambio	0044-7447	0.007463	181.878048780488
"American journal of human genetics"	0002-9297	0.120156	67.1898928024502
"American journal of hypertension"	0895-7061	0.017359	104.074576271186
(....)

Here is the kind of figure I got:

As far as I remember, "Cell" is the point having the highest eigenfactor.


Note: pubmed contains some errors: e.g. received > accepted (http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=20591334&retmode=xml) or some dates in the future: ( http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=12921703&retmode=xml )


That's it,

Pierre

Controlling IGV through a Port: my notebook.

A protocol for interacting with the The Integrative Genomics Viewer (IGV) is described here: http://www.broadinstitute.org/igv/PortCommands. So, you can save some pictures of a genomic region without interacting with IGV.

Via a shell script

$ cat script.sh

mkdir -p /tmp/igv
sleep 2
echo "snapshotDirectory /tmp/igv"
sleep 2
echo "goto chr3:100"
sleep 2
echo "snapshot"
sleep 2
echo "goto chr3:200-300"
sleep 2
echo "snapshot"
sleep 2

invoke the script

$ sh script.sh |  telnet 127.0.0.1 60151
Trying 127.0.0.1...
Connected to srv-clc-02.irt.univ-nantes.prive (127.0.0.1).
Escape character is '^]'.
INFO [2011-07-27 17:58:16,680]  [CommandExecutor.java:124] [Thread-6]  OK
OK
INFO [2011-07-27 17:58:18,685]  [CommandExecutor.java:124] [Thread-6]  OK
OK
INFO [2011-07-27 17:58:18,687]  [MacroSnapshotAction.java:85] [Thread-6]  Snapshot: chr3_80_119.png
INFO [2011-07-27 17:58:20,787]  [CommandExecutor.java:124] [Thread-6]  OK
OK
INFO [2011-07-27 17:58:22,792]  [CommandExecutor.java:124] [Thread-6]  OK
OK
INFO [2011-07-27 17:58:22,794]  [MacroSnapshotAction.java:85] [Thread-6]  Snapshot: chr3_200_300.png
Connection closed by foreign host.

Via java

The code

import java.io.*;
import java.net.*;
class Test
{
public static void main(String[] args) throws Exception
 {
 Socket socket = new Socket("127.0.0.1", 60151);
        PrintWriter out = new PrintWriter(socket.getOutputStream(), true);
        BufferedReader in = new BufferedReader(new InputStreamReader(socket.getInputStream()));


        out.println("snapshotDirectory /tmp/igv");
  System.out.println(in.readLine());
        out.println("goto chr3:100");
        System.out.println(in.readLine());
 
      out.println("snapshot");
 System.out.println(in.readLine());

 in.close();
 out.close();
 socket.close();
 }
}

Compile and execute:

$ javac Test
$ java Test
INFO [2011-07-27 18:01:15,706]  [CommandExecutor.java:124] [Thread-6]  OK
OK

INFO [2011-07-27 18:01:17,711]  [CommandExecutor.java:124] [Thread-6]  OK
OK

INFO [2011-07-27 18:01:17,729]  [MacroSnapshotAction.java:85] [Thread-6]  Snapshot: chr3_80_119.png
INFO [2011-07-27 18:01:20,533]  [CommandExecutor.java:124] [Thread-6]  OK
OK

An interactive 'dialog' generating a SAM Flag

The following shell script uses the dialog utility to generate a numeric Sam flag.

$ sh selectsam.sh 
      ┌───────────────────────SAM FLAGS──────────────────────────┐
      │ SELECT FLAGS                                             │  
      │ ┌──────────────────────────────────────────────────────┐ │  
      │ │ [X] 1     Read Paired                                │ │  
      │ │ [ ] 2     Read mapped in proper pair                 │ │  
      │ │ [X] 4     Read unmapped                              │ │  
      │ │ [ ] 8     Mate unmapped                              │ │  
      │ │ [ ] 16    Read reverse strand                        │ │  
      │ │ [X] 32    Mate reverse strand                        │ │  
      │ │ [ ] 64    First in pair                              │ │  
      │ │ [X] 128   Second in pair                             │ │  
      │ │ [ ] 256   Not primary alignment                      │ │  
      │ │ [ ] 512   Read fails platform/vendor quality checks  │ │  
      │ │ [ ] 1024  Read is PCR or optical duplicate           │ │  
      │ └─────↓(+)─────────────────────────────────────────────┘ │  
      │                                                          │  
      │                                                          │  
      ├──────────────────────────────────────────────────────────┤  
      │                         <  OK  >                         │  
      └──────────────────────────────────────────────────────────┘  
        
$ 165

Source available at: https://github.com/lindenb/samtools-utilities/blob/master/script/selectflag.sh

That's it,

Pierre

I can't save you, but I can help you: reverse-complementing a DNA in OpenOffice

People in my lab are using "Microsoft Word" to edit and annotate their sequences. Just like Neil, I can't save them but I can help them: here is an OpenOffice / LibreOffice macro reverse-complementing the current selected text.

• open libreoffice/openoffice
• Open menu "Tools / Macros / Organize macros / Basic...
• Select "My Macros/Standard" and click on "New"
• Copy+paste my macro here
• Click on the top button "compile"
• Close the dialog
• Menu "Tools/Customize" , "Keyboard" tab, "Toolbar content" . Button "Add... " / Category "Libre Office Macros" . Select "My Macro/Standard/Modulexxx"/ReverseComplementSelection". Click on "Modify" to assign an icon to this new button
• There is now a new button in the toolbar. Clicking on that button reverse-complements the selected text.

That's it,

Pierre

PS: Hum ? what did you say, they use Microsoft Word ? Not OpenOffice ? pfff....

Playing with the Gimp server: my notebook

In the following post, I'll show how the Gimp can be used as a server that will read and execute some statements in the scheme programming language. The scheme script will be used to downlad, resize and filter an image from the web.

Starting the Gimp Server

Go in menu Filters→Script-Fu→Start Server

The original image

(3156 x 2538)Barbara McClintock in the lab at Cold Spring Harbor in 1947

The script

Here is the scheme script:

The java client

The following java client will send the previous scheme script to the gimp server. The simple protocol used by GIMP is described on this page.

>javac GimpClient.java
>java GimpClient input.scm
Success

The result

That's it,


Pierre