Difference between revisions of "Talk:Martin Jambon"

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'''[[User:Evgeny Fadeev|Evgeny Fadeev]] 21:35, 10 April 2008 (EDT)''' Just installed <nowiki><biblio></nowiki> on [nmrwiki.org nmrwiki.org]. Question: what happens if isbn limit is reached? Thanks!!!
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'''[[User:Evgeny Fadeev|Evgeny Fadeev]] 21:35, 10 April 2008 (EDT)''' Just installed <nowiki><biblio></nowiki> on [http://nmrwiki.org nmrwiki.org]. Question: what happens if isbn limit is reached? Thanks!!!
  
 
'''[[User:Ilya|Ilya]] 15:42, 22 August 2007 (EDT)''': Hi Martin, your Biblio extension has stopped working.  See http://wikiomics.org/wiki/Searching_for_3D_functional_sites_in_a_protein_structure and http://openwetware.org/wiki/Registry_of_standard_biological_parts/PCR-based_assembly.  OpenWetWare is running the latest version of it (0.8.1).  Also, I've tested the NCBI web service API with their [http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#DemonstrationPrograms demo scripts] and it seems to be working fine.  Any idea what could be wrong and how to fix it?  Thanks.
 
'''[[User:Ilya|Ilya]] 15:42, 22 August 2007 (EDT)''': Hi Martin, your Biblio extension has stopped working.  See http://wikiomics.org/wiki/Searching_for_3D_functional_sites_in_a_protein_structure and http://openwetware.org/wiki/Registry_of_standard_biological_parts/PCR-based_assembly.  OpenWetWare is running the latest version of it (0.8.1).  Also, I've tested the NCBI web service API with their [http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#DemonstrationPrograms demo scripts] and it seems to be working fine.  Any idea what could be wrong and how to fix it?  Thanks.

Revision as of 18:35, 10 April 2008

Evgeny Fadeev 21:35, 10 April 2008 (EDT) Just installed <biblio> on nmrwiki.org. Question: what happens if isbn limit is reached? Thanks!!!

Ilya 15:42, 22 August 2007 (EDT): Hi Martin, your Biblio extension has stopped working. See http://wikiomics.org/wiki/Searching_for_3D_functional_sites_in_a_protein_structure and http://openwetware.org/wiki/Registry_of_standard_biological_parts/PCR-based_assembly. OpenWetWare is running the latest version of it (0.8.1). Also, I've tested the NCBI web service API with their demo scripts and it seems to be working fine. Any idea what could be wrong and how to fix it? Thanks.

Julius B. Lucks 10:40, 10 July 2007 (EDT): Hi Martin. I am loving your biblio extension, and I am starting to use it a lot on OWW. How easy would it be to extend its functionality to include articles outside of PubMed. In particular, I am referring to content on arXiv.org, which has been used by physicists as a pre-print server for quite some time now. (In fact, Nature just annonced an effort to make an arXiv-like site soon). The arXiv also has a quantitative biology section which is starting to see a lot of bio-related articles relevant to oww interests.

I see that you are using the PubMed SOAP API to get your info. The arXiv currently doesn't have such an API - would it still be possible to make the biblio extension work? I appreciate your time! - Julius


Austin 14:04, 19 June 2006 (EDT): Biblio 0.7.4 on OWW with MediaWiki 1.6.7 appears to have problems with the cite tag. See the Sandbox for an example.

I'll see what I can do. Thanks. --Martin 14:37, 19 June 2006 (EDT)
I discovered that the math formulas don't work on the old pages (the ones which were there before the upgrade like Sandbox), both on my local wiki and here. For example, the current talk page is new, and it works: <math>\sqrt{\pi}</math> gives '"`UNIQ--postMath-00000001-QINU`"'. --Martin 15:50, 19 June 2006 (EDT)
It seems to work similarly with the "cite" tags: <cite>blabla</cite> gives [1]. --Martin 15:50, 19 June 2006 (EDT)
On my personal quick upgrade of Mediawiki I did not run any particular upgrade script (and I am pretty sure that I should), and I don't know what you did here. I did not perform any upgrade of MediaWiki other than that before, so I can't really help you now - sorry... --Martin 15:50, 19 June 2006 (EDT)

Biblio & Show / Hide

Question

Hi, I would like to know if it is possible to do the following. I think it's a really useful way of displaying a bibliography:

<showhide>2002-2007 Publications__HIDER__ 
<hide>
<biblio>
#[[Streptomyces:PublicationsKelemen]]
</biblio>
</hide>
</showhide>

<showhide>2002-2007 Publications__HIDER__ <hide>

  1. - Kelemen, G.H.==

    Streptomyces @ UEA

    Home        Research        Research Groups        Publications        Resources        Meetings        Links        Contact

    <html> <!-- START OF STATCOUNTER CODE --> <script type="text/javascript" language="javascript"> var sc_project=2419278; var sc_invisible=1; var sc_partition=22; var sc_security="abf914b3"; </script> <script type="text/javascript" language="javascript" src="http://www.statcounter.com/counter/counter.js"></script><noscript><a href="http://www.statcounter.com/" target="_blank"><img src="http://c23.statcounter.com/counter.php?sc_project=2419278&amp;java=0&amp;security=abf914b3&amp;invisible=0" alt="web metrics" border="0"></a> </noscript> <a href=http://www.theresonly1.eu><font color=white> </font> </a> <a href=http://www.theresonly1.co.uk><font color=white> </font> </a> <a href=http://www.rahart.eu><font color=white> </font> </a> <a href=http://www.jimandsarah.plus.com><font color=white> </font> </a> <a href=http://www.uea.ac.uk/~b101><font color=white> </font> </a> <a href=http://www.uea.ac.uk/~tdc07rfu><font color=white> </font> </a> <!-- END OF STATCOUNTER CODE--> </html>

    Kelemen, G.H.
     2000 - Present
    1. Gaskell AA, Crack JC, Kelemen GH, Hutchings MI, and Le Brun NE. RsmA is an anti-sigma factor that modulates its activity through a [2Fe-2S] cluster cofactor. J Biol Chem. 2007 Oct 26;282(43):31812-20. DOI:10.1074/jbc.M705160200 | PubMed ID:17766240 | HubMed [Gaskell-JBiolChem-2007]
    2. Dalton KA, Thibessard A, Hunter JI, and Kelemen GH. A novel compartment, the 'subapical stem' of the aerial hyphae, is the location of a sigN-dependent, developmentally distinct transcription in Streptomyces coelicolor. Mol Microbiol. 2007 May;64(3):719-37. DOI:10.1111/j.1365-2958.2007.05684.x | PubMed ID:17462019 | HubMed [Dalton-MolMicro-2007]
    3. Hunt AC, Servín-González L, Kelemen GH, and Buttner MJ. The bldC developmental locus of Streptomyces coelicolor encodes a member of a family of small DNA-binding proteins related to the DNA-binding domains of the MerR family. J Bacteriol. 2005 Jan;187(2):716-28. DOI:10.1128/JB.187.2.716-728.2005 | PubMed ID:15629942 | HubMed [Hunt-JBac-2005]
    4. Traag BA, Kelemen GH, and Van Wezel GP. Transcription of the sporulation gene ssgA is activated by the IclR-type regulator SsgR in a whi-independent manner in Streptomyces coelicolor A3(2). Mol Microbiol. 2004 Aug;53(3):985-1000. DOI:10.1111/j.1365-2958.2004.04186.x | PubMed ID:15255907 | HubMed [Traag-MolMicro-2004]
    5. Viollier PH, Kelemen GH, Dale GE, Nguyen KT, Buttner MJ, and Thompson CJ. Specialized osmotic stress response systems involve multiple SigB-like sigma factors in Streptomyces coelicolor. Mol Microbiol. 2003 Feb;47(3):699-714. PubMed ID:12535070 | HubMed [Viollier-MolMicro-2003]
    6. Kelemen GH, Viollier PH, Tenor J, Marri L, Buttner MJ, and Thompson CJ. A connection between stress and development in the multicellular prokaryote Streptomyces coelicolor A3(2). Mol Microbiol. 2001 May;40(4):804-14. PubMed ID:11401688 | HubMed [Kelemen-MolMicro-2001]
    All Medline abstracts: PubMed | HubMed

    <wikionly> Edit Kelemen Publication List </wikionly>


    [Publications]

</hide> </showhide>

I can get the biblio tags to work fine & display the list on Streptomyces:PublicationsKelemen page, just not in a useful show/hide display. I thought this would be good to show publications in 5 year groups that a reader could show/hide rather than one great long list. Could this be an issue with biblio or the show / hide tags? I'd be grateful for any helpful comments.

Thanks, Jim @ Streptomyces 17:37, 15 March 2007 (EDT)

I see the problem. It seems that the showhide extension doesn't process syntax extensions. It may be tricky to do so, I don't know, I will forward this to whomever wrote this showhide thingy. --Martin 18:20, 15 March 2007 (EDT)

Thanks

Thanks for taking a look Martin :-) Jim @ Streptomyces 06:32, 16 March 2007 (EDT)

Additional Cite Tags?

Hi Martin,

Thanks for your help before, I now have Biblio nicely nested in between some Toggle tags.
I now have another question. Would it be possible to create an additional pair of cite tags, that when used, would display the original text of the key. Currently to create a reference I type <biblio> # Dalton-MolMicro-2007 pmid=17462019 </biblio> . To cite this reference I nest the key in cite tags: <cite> Dalton-MolMicro-2007 </cite> and this displays the inline citation as [1]. I would now like to use different tags e.g. <citeref> </citeref> to display the inline citation as [Dalton-MolMicro-2007].
I know the numbering system has its advantages in that the text is easier to read. However, the naming system would be useful for large blocks of text, or text with lots of citations; so the reader doesn't have to keep clicking on the [1] link and scroll back up the page. I hope this makes sense and is something that will be considered.
I find this a brilliant extension and very useful. Thanks for reading, Jim @ Streptomyces 09:17, 3 May 2007 (EDT)

I guess that could be done easily, by editing the PHP file. However I don't have much time now to do it myself. --Martin 06:24, 7 May 2007 (EDT)