User talk:Jakob Suckale: Difference between revisions

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<b>please put your comment at the top (easier to find)</b>
== Archive ==
 
older conversations moved to [[User talk:Jakob Suckale archive]]
 
==PhDTemplate - BibTeX Errors==
I found a typo in the Template:
when wanting to create the bibliography i always got a bibtex error (bibtex finished with exit code 2) - until i found out that the line "\bibliographystyle{Latex/Classes/PhDbiblio-url2}" actually links to a file that does not exist - at least not named like that.
But there is a CUEDbiblio-url2 - and after renaming that it worked. Same for the other PhDbiblio-xy.
 
Afterwards i got the error "package natbib error: Bibliography not compatible with author-year citations" - which can be solved by editing the Latex/Classes/PhDthesisPSnPDF.cls - line "\usepackage[round, sort, numbers, authoryear ]{natbib}" - deleting the authoryear got it working.
 
Just wanted to let you know. And thanks for that template. Saves me a lot of time. [[User:Matthias_Gerndt|Matthias]]
 
==PhDTemplate and chinese characters==
Hi, I was wondering whether you had an idea on how I could use chinese characters in the template. I tried several things but it all boils down to using XeLatex which won't work with the template or using inputenc which somehow doesn't seem to be used by the template. Any way around this? Thanks in advance. - [[User:Louis_Drounau|Louis]]
 
:Sorry, no idea. I would ask at on of the latex forums. [[User:Jakob Suckale|Jakob]] 12:45, 27 April 2010 (EDT)
 
Ok. Although my question was more about the parameters of the template: I found lots of way to use Chinese characters in latex files but they don't seem to work with the template...


== Materials ==
== Materials ==
Line 24: Line 8:


I think we can do the same for protocols as well if this gets moving.
I think we can do the same for protocols as well if this gets moving.


==Latex Thesis Template==
==Latex Thesis Template==
Line 38: Line 23:
Best, *'''[[User:Louis Drounau|Louis Drounau]] 06:31, 25 April 2009 (EDT)''':
Best, *'''[[User:Louis Drounau|Louis Drounau]] 06:31, 25 April 2009 (EDT)''':


==RNA blotting==
Hi Jakob, I agree regarding the naming of RNA/Northern blotting.  I moved the content to [[RNA blot (Northern)]] and made a Northern blot a redirect (previously it was the other way around).


Thanks!
==PhDTemplate and chinese characters==
Hi, I was wondering whether you had an idea on how I could use chinese characters in the template. I tried several things but it all boils down to using XeLatex which won't work with the template or using inputenc which somehow doesn't seem to be used by the template. Any way around this? Thanks in advance. - [[User:Louis_Drounau|Louis]]


Barry
:Sorry, no idea. I would ask at on of the latex forums. [[User:Jakob Suckale|Jakob]] 12:45, 27 April 2010 (EDT)


Ok. Although my question was more about the parameters of the template: I found lots of way to use Chinese characters in latex files but they don't seem to work with the template...


==Pubmed==


Hi Jakob, I'm a biotech Ph.D student at Seoul National University. Currently we're using 3D protein structural prediction software to get an idea about the shape of the protein we're isolating.
==PhDTemplate - BibTeX Errors==
I found a typo in the Template:
when wanting to create the bibliography i always got a bibtex error (bibtex finished with exit code 2) - until i found out that the line "\bibliographystyle{Latex/Classes/PhDbiblio-url2}" actually links to a file that does not exist - at least not named like that.
But there is a CUEDbiblio-url2 - and after renaming that it worked. Same for the other PhDbiblio-xy.


What I was wondering was, how accepted are current 3D computer structural predictions in the literature? Specifically I'm using I-Tasser (Zhang lab) and Phyre. I tried to do a search on Pubmed them but only came up with bioinformatics results.
Afterwards i got the error "package natbib error: Bibliography not compatible with author-year citations" - which can be solved by editing the Latex/Classes/PhDthesisPSnPDF.cls - line "\usepackage[round, sort, numbers, authoryear ]{natbib}" - deleting the authoryear got it working.


Can you show me how to do a Pubmed search that returns me results where people have mentioned these structural prediction programs in their papers? Specifically, those papers that do not have a focus on the bioinformatics or programming side of it. I am wondering how legitimate and accepted they are by the scientific community for use in application. For example, from the structural results, I'm starting to believe that our candidate might be a mimic of a host protein.
Just wanted to let you know. And thanks for that template. Saves me a lot of time. [[User:Matthias_Gerndt|Matthias]]
 
Also, what is your opinion on the reliability of such software these days?
 
Thank you,
 
- Lee
 
==Northern Blot==
Hi Jakob, I saw the ratings you added to the External links on the [[RNA blot (Northern)|Northern page]].  What was the ranking criteria?  If you could provide a few sentences on how you think this should work maybe others could rank other protocols they link to.  Nice work on the page by the way.  Thanks!  Barry
 
: Hi Barry, it's quite a simple procedure. I prowl the web for suitable pages to link to the protocol. I visit every page and evaluate the relevance, content, and design more or less in that order and then I attach the star ratings according to the suitability of the web site for the openwetware page in question. Should this info be moved to the [[Protocols/Consensus template|consensus protocol]] page as a suggestion/option?
 
* [[Image:3stars.png]] excellent website, detailed information, very useful link
* [[Image:2stars.png]] good website, some information, useful link
* [[Image:1stars.png]] ok website, a few pieces of info, secondary link
 
== sc ==
*'''[[User:Austin J. Che|Austin Che]] 12:17, 14 May 2008 (EDT)''': the steering committee meeting is going on right now in case you're interested
*'''[[User:Austin J. Che|Austin Che]] 12:32, 14 May 2008 (EDT)''': Go to your preferences and change your password (you can change it to the same one you have currently) and try logging in again. You can also connect with any jabber client: [[Help:Chat]].
 
== icons ==
 
Hi Jakob,
 
I just added your nice icons to the [[Protocols/Consensus template | protocol template]] so that one could see if people make use of it or prefer to omit them.
 
Grüsse nach Dresden,
'''[[User:Torsten Waldminghaus|Torsten Waldminghaus]] 07:31, 8 May 2008 (EDT)''':
 
==Papers==
*'''[[User:Barry Canton|BC]] 08:57, 13 October 2007 (CDT)''': Hey Jakob, saw Papers and liked it.  However, I couldn't find evidence of it supporting export of a biblography to word or latex.  Until it gets such a feature, I expect I'll stick with [http://bibdesk.sourceforge.net/ Bibdesk].
==Statistics portal==
*'''[[User:Reshma P. Shetty|Reshma]] 12:23, 7 September 2007 (EDT)''': Hey Jasu, I think your statistics portal is really useful.  On a whim, I decided to try out a redesign of the page. Basically, I tried to
*#change the layout so that you don't have to scroll down in order to see the useful information. 
*#change the colors to be more like OWW colors
*#use more wiki code and less html to make it more amenable to editing
What do you think?  Please feel free to change it back if you don't like it.  Also, another idea is to [[Help:Renaming pages|move the page]] to [[Statistics]] ... the shorter name might be easier to type and remember?  Anyway, let me know what you think.
 
* I like the layout suggestion that you made. You have a good point with the content being accessible w/o scrolling. Made some small changes, e.g. reduced OWW graphic to make it flush w the table below, removed blue bg from below the 3D Gaussian - didn't go well w the red, and enlarged the graphic slightly. I also think the cell classes have slightly too little cellpadding. Looks a bit crowded. Tried to override it, but that didn't work w/o taking away the class. Statistics portal to Statistics sounds good. Simpler is better. We could do w some more content ;-) There are some suggestions in the discussion which I couldn't integrate, yet. All the best, [[User:Jasu|Jasu]] 19:33, 7 September 2007 (EDT)
**'''[[User:Reshma P. Shetty|Reshma]] 11:14, 8 September 2007 (EDT)''': Sounds good.  I moved the page to [[Statistics]].


== ethics portal ==
:* Excellent. Thanks, for fixing those bugs. Have you considered [http://openwetware.org/wiki/Image:PhDtemplateLATEX.zip uploading a new version] with your fixes. I'm sure the community would appreciate it. [[User:Jakob Suckale|JS]]


Wow, this is really neat.  Perhaps we can put a spotlight on it soon and ask others for help as well.  Thanks for all your efforts in putting this stuff up here.  If you are interested, you should consider joining the [[OpenWetWare:Steering committee|Steering Committee]] as well if you are interested in participating in discussions on where OWW should be going in the future.


--[[Sri Kosuri]] ([[User talk:Skosuri|talk]]) 15:27, 6 March 2007 (EST)
==Accents==
Hey Jakob. Another year, another thesis and apparently I just can't do without this template! Now, I've found a new dilemma for you: I'm asked to write in French this time and I need to make a few adjustments to the template. In the chapters, I'm keeping it easy by write \'e instead of é, for example, and it works fine. But I also need to change the structure, words like "glossary" or parts like "a thesis submitted...". I found where to do that (PhDthesisPSnPDF.cls) but as soon as I get an accent in there, the whole thing stops working. Any thoughts? [[User:Louis Drounau|Louis]]


==welcome==
* I'm sorry I don't. If I were in your situation I would post for help in the LaTeX forums where the real geeks are to be found, not some light weight, somewhat expert users like me. --[[User:Jakob Suckale|- JS]] 09:11, 22 September 2011 (EDT)
Hi there, Jasu, and welcome to [[Main Page|OpenWetWare]]! We hope you find it to your liking. Here's a couple links you might find useful:
*[[Help:contents|General help page]]
*[[OpenWetWare:Getting started|Getting started on OpenWetWare]]
*[[Simple wiki editing examples|How to edit a page]]
*[[OpenWetWare:FAQ|FAQ]]
*[[Etiquette]]
Also, please be aware that the general [[Help:page naming conventions|naming convention]] when creating a new page for a lab is <code>Labname:Page name</code>. If you have any questions, feel free to contact me on my talk page. Good luck!


--[[Sri Kosuri]] ([[User talk:Skosuri|talk]]) 23:04, 7 December 2006 (EST)


ps. I noticed that you are pretty adept at wiki-ing.  Keep up the good work.  It's nice to see people really helping out the community pages!
== Exporting a .bib file from Papers ==


== getting started ==
Hello Jakob,
Thanks for the PhD template that you uploaded. Being new to LaTeX, I don't know if it is possible to use a .bib library file exported from a PDF organizer program called Papers (by Mekentosj). Have you encountered this before?
I tried replacing the contents of the references.bib file you had in your template with those exported from Papers. I changed the citations and all but the changes don't reflect in the References page.
Thanks a lot and any help would be greatly appreciated!
[[User:Angelo Porciuncula|Angelo Porciuncula]]
SPAIN


Just getting started here and eager to find out about OWW. Jasu 13:25, 20 June 2006 (EDT)
* Hi Angelo, this should be possible. I, personally, haven't used Papers this way but I'm aware of the BibTex export function. Instead I used BibDesk since Papers wasn't sufficiently well developed at this point. So, unfortunately, I can only tell you that it should work in principle. You would need to exchange the .bib file and the references to the bib file in the text itself. Then, after re-compilation, you should see the changes. Sorry, don't have time to go into more detail. Ask friends from computer sciences or physics at your uni. Saludos, --[[User:Jakob Suckale|- JS]] 09:29, 22 September 2011 (EDT)

Latest revision as of 06:32, 22 September 2011

Archive

older conversations moved to User talk:Jakob Suckale archive

Materials

  • Bill Flanagan (OpenWetWare.org at MIT) 14:00, 29 April 2009 (EDT) * Thanks for the continued 'material' advice. I'm still working on the changes we've discussed. No population of equipment as a new set of categories or search tags until at least 'Material' has been improved.

I think we can do the same for protocols as well if this gets moving.


Latex Thesis Template

Hi Jakob, Thanks for working on that thesis template, it's a great help to me at the moment. However, I'm running through the same difficulties you seemed to be having with the glossary. You said you'd found a way to deal with it. Could you explain to me how you did it please? Thanks in advance.

EDIT:

Hi, Thanks for your message, although I'm not sure my level is good enough to follow your explanations. I guess I'll just procrastinate a little longer before I seriously try to see how that glossary works. One more question though: the roman numbering starts at the begining of the document (pages i and ii) but simply disappears on the front matter pages (abstract, dedication, acknowledgement) and re-appears on the List of Content (page iii). Any idea how to have the numbers on front matter pages? Thanks in advance. PS: just a little correction, on the Abstract page, \end{abstractlongs} should be \end{abstractslong}

Best, *Louis Drounau 06:31, 25 April 2009 (EDT):


PhDTemplate and chinese characters

Hi, I was wondering whether you had an idea on how I could use chinese characters in the template. I tried several things but it all boils down to using XeLatex which won't work with the template or using inputenc which somehow doesn't seem to be used by the template. Any way around this? Thanks in advance. - Louis

Sorry, no idea. I would ask at on of the latex forums. Jakob 12:45, 27 April 2010 (EDT)

Ok. Although my question was more about the parameters of the template: I found lots of way to use Chinese characters in latex files but they don't seem to work with the template...


PhDTemplate - BibTeX Errors

I found a typo in the Template: when wanting to create the bibliography i always got a bibtex error (bibtex finished with exit code 2) - until i found out that the line "\bibliographystyle{Latex/Classes/PhDbiblio-url2}" actually links to a file that does not exist - at least not named like that. But there is a CUEDbiblio-url2 - and after renaming that it worked. Same for the other PhDbiblio-xy.

Afterwards i got the error "package natbib error: Bibliography not compatible with author-year citations" - which can be solved by editing the Latex/Classes/PhDthesisPSnPDF.cls - line "\usepackage[round, sort, numbers, authoryear ]{natbib}" - deleting the authoryear got it working.

Just wanted to let you know. And thanks for that template. Saves me a lot of time. Matthias

  • Excellent. Thanks, for fixing those bugs. Have you considered uploading a new version with your fixes. I'm sure the community would appreciate it. JS


Accents

Hey Jakob. Another year, another thesis and apparently I just can't do without this template! Now, I've found a new dilemma for you: I'm asked to write in French this time and I need to make a few adjustments to the template. In the chapters, I'm keeping it easy by write \'e instead of é, for example, and it works fine. But I also need to change the structure, words like "glossary" or parts like "a thesis submitted...". I found where to do that (PhDthesisPSnPDF.cls) but as soon as I get an accent in there, the whole thing stops working. Any thoughts? Louis

  • I'm sorry I don't. If I were in your situation I would post for help in the LaTeX forums where the real geeks are to be found, not some light weight, somewhat expert users like me. --- JS 09:11, 22 September 2011 (EDT)


Exporting a .bib file from Papers

Hello Jakob, Thanks for the PhD template that you uploaded. Being new to LaTeX, I don't know if it is possible to use a .bib library file exported from a PDF organizer program called Papers (by Mekentosj). Have you encountered this before? I tried replacing the contents of the references.bib file you had in your template with those exported from Papers. I changed the citations and all but the changes don't reflect in the References page. Thanks a lot and any help would be greatly appreciated! Angelo Porciuncula SPAIN

  • Hi Angelo, this should be possible. I, personally, haven't used Papers this way but I'm aware of the BibTex export function. Instead I used BibDesk since Papers wasn't sufficiently well developed at this point. So, unfortunately, I can only tell you that it should work in principle. You would need to exchange the .bib file and the references to the bib file in the text itself. Then, after re-compilation, you should see the changes. Sorry, don't have time to go into more detail. Ask friends from computer sciences or physics at your uni. Saludos, --- JS 09:29, 22 September 2011 (EDT)
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