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From: Andrew S. <as...@gn...> - 2007-06-26 17:17:48
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Hi Ian, Super, I appreciate the detailed responses from you and Martin, and glad to hear that the multi-URI issue is high on the radar screen. (A related issue you're probably already aware of. Some publishers appear to put session-specific fields into their URI. For example, the second link on http://www.connotea.org/user/asutest no longer works. I've added this to the "Possible Problems" section of the wiki.) Also glad to hear that you will post the updated source and the internal NPG/Neoreality development plan on the wiki. If I can add another suggestion, I would lobby for the release of the updated source code sooner rather than later, even if the corresponding development plan is not ready. The rate-limiting step right now appears to be the number of people looking at and working on the code, and not a lack of coordination. I think at least in the short term, maybe we might focus our efforts on the session-URI issue above, John-Paul could work on the Shibboleth integration that he cares about, etc etc. And I think it'd be pretty unlikely that we came up with conflicting or overlapping solutions. My two cents... Please send out an update when you have any specific timelines or progress. Cheers, -andrew > -----Original Message----- > From: con...@li... [mailto:connotea- > cod...@li...] On Behalf Of Mulvany, Ian > Sent: Tuesday, June 26, 2007 2:53 AM > To: con...@li... > Subject: Re: [Connotea-code-devel] Connotea-code-devel Digest, Vol > 14,Issue 14 >=20 > Hi Andrew, >=20 > I'll start with your last point first. We will be resolving the buggotea > problem for articles that have identifiers, be those PMID's or DOI's. We > use > an MD5 hash of the URI of a resource as the key identifier in the MySQL db > for each bookmark, and the way the code is written at the moment makes it > a > very difficult task to change this, but we will be able to at least > pseudo-merge resources that have the identifiers mentioned. >=20 > The first part of your post is very interesting. You are right about the > development taking place mostly between NPG and Neo-reality. There was a > slow-down in development at the beginning of this year as we had a change > over in people. I've joined NPG to work on Connotea, and have been writing > up a plan for it's development. I'm really keen to encourage as much > participation as I can. We have moved the live Connotea Code into a Darcs > repository to simplify distributed development and we should be releasing > a > new OS release within a few weeks. >=20 > I think you idea of opening up the plan is also a very good one, and I > will > put up on the Connotea Wiki what we will be planning to do and when, along > with what we would like to do, but possibly don't have time for, when I > have > the plan finalised. >=20 > - Ian >=20 >=20 > On 25/6/07 20:05, "con...@li..." > <con...@li...> wrote: >=20 > > Send Connotea-code-devel mailing list submissions to > > con...@li... > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel > > or, via email, send a message with subject or body 'help' to > > con...@li... > > > > You can reach the person managing the list at > > con...@li... > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Connotea-code-devel digest..." > > > > > > Today's Topics: > > > > 1. development questions (Andrew Su) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 25 Jun 2007 10:39:14 -0700 > > From: "Andrew Su" <as...@gn...> > > Subject: [Connotea-code-devel] development questions > > To: <con...@li...> > > Message-ID: > > <190...@EX...> > > Content-Type: text/plain; charset=3D"us-ascii" > > > > Hello, > > > > > > > > I've been lurking on both the connotea mailing lists for a while now and > > I thought I'd pose a basic question... Is there a public plan for > > future connotea development? I think it's great that the code is open > > source, but it appears that coding is still being primarily done by > > Nature and NeoReality folks (not sure if the latest enhancements are > > posted to sourceforge though). Is there a desire to open up the > > development team to include other developers who want to see connotea > > mature faster? I've been helping to explore thesis project ideas for a > > couple bioinformatics masters students, and collaborating on connotea > > may be an interesting prospect. > > > > > > > > And on another note, does anyone have a good feeling for the reasons why > > connotea is not being used more? Of course, I'm asking this question > > not knowing anything about usage statistics, only that I don't know > > anyone personally (myself included) that uses it in production. My > > reason? What someone referred to as Buggotea > > (http://www.nodalpoint.org/2007/03/30/so_connotea_or_citeulike), which > > really hinders the social aspect of the site. > > > > > > > > Any thoughts appreciated... > > > > > > > > Cheers, > > > > -andrew > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > > > ------------------------------ > > > > ------------------------------------------------------------------------ > - > > This SF.net email is sponsored by DB2 Express > > Download DB2 Express C - the FREE version of DB2 express and take > > control of your XML. No limits. Just data. Click to get it now. > > http://sourceforge.net/powerbar/db2/ > > > > ------------------------------ > > > > _______________________________________________ > > Connotea-code-devel mailing list > > Con...@li... > > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel > > > > > > End of Connotea-code-devel Digest, Vol 14, Issue 14 > > *************************************************** >=20 >=20 > -- > Ian Mulvany > i.m...@na... > +44(0)2078434756 > www.nature.com > www.connotea.org > -- >=20 >=20 >=20 > ************************************************************************ ** > ****** > DISCLAIMER: This e-mail is confidential and should not be used by anyone > who is > not the original intended recipient. If you have received this e-mail in > error > please inform the sender and delete it from your mailbox or any other > storage > mechanism. Neither Macmillan Publishers Limited nor any of its agents > accept > liability for any statements made which are clearly the sender's own and > not > expressly made on behalf of Macmillan Publishers Limited or one of its > agents. > Please note that neither Macmillan Publishers Limited nor any of its > agents > accept any responsibility for viruses that may be contained in this e-mail > or > its attachments and it is your responsibility to scan the e-mail and > attachments (if any). No contracts may be concluded on behalf of Macmillan > Publishers Limited or its agents by means of e-mail communication. > Macmillan > Publishers Limited Registered in England and Wales with registered number > 785998 > Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS > ************************************************************************ ** > ****** >=20 > ------------------------------------------------------------------------ - > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Connotea-code-devel mailing list > Con...@li... > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel |
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From: Paolo M. <pao...@du...> - 2007-06-26 14:58:07
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I'll second the desire for Shibboleth integration with Connotea. I think it would help with adoption if people could use existing authentication credentials instead of creating a separate account. Also, I think you should not limit Connotea's potential target audience to the sciences only. We've been encouraging scholars in all disciplines to consider it for their use here at Duke, as it is potentially just as useful to them as it is to scientists. CiteULike seems to have more of a critical mass among the sciences already, so other disciplines may be the place where Connotea can make a bigger difference. With respect to the question about why Connotea is not being used more, I think it would be useful to have more examples of how it might be used for instruction as well as research. We've been talking to librarians and faculty here about using it as the basis for creation of reading lists for courses or project teams - create a group and/or specific tag in Connotea, add citations to them, and then embed an RSS feed of the tag/group in your Blackboard course site, web page, etc., and the reading list gets updated every time you add something new to Connotea. We've been meaning to write up some tips on how to do this, but haven't had a chance yet. It would be great to have more stuff like this on the connotea.org site - helping people think through and understand the many ways this tool could be used. Thanks... -- Paolo John-Paul Robinson wrote: > I've been a lurker for a while too and have enjoyed this thread and > update. I currently use connotea-code for an internal bookmarking > service. I just wanted to put a vote in for more project transparency. > > I'm interested in contributing to a modification to support the use of > webiso for authnz (Shibboleth to be specific) so that it can be > integrated with our local collaboration environment. > > ~jpr > > Mulvany, Ian wrote: >> Hi Andrew, >> >> I'll start with your last point first. We will be resolving the buggotea >> problem for articles that have identifiers, be those PMID's or DOI's. We use >> an MD5 hash of the URI of a resource as the key identifier in the MySQL db >> for each bookmark, and the way the code is written at the moment makes it a >> very difficult task to change this, but we will be able to at least >> pseudo-merge resources that have the identifiers mentioned. >> >> The first part of your post is very interesting. You are right about the >> development taking place mostly between NPG and Neo-reality. There was a >> slow-down in development at the beginning of this year as we had a change >> over in people. I've joined NPG to work on Connotea, and have been writing >> up a plan for it's development. I'm really keen to encourage as much >> participation as I can. We have moved the live Connotea Code into a Darcs >> repository to simplify distributed development and we should be releasing a >> new OS release within a few weeks. >> >> I think you idea of opening up the plan is also a very good one, and I will >> put up on the Connotea Wiki what we will be planning to do and when, along >> with what we would like to do, but possibly don't have time for, when I have >> the plan finalised. >> >> - Ian >> >> >> On 25/6/07 20:05, "con...@li..." >> <con...@li...> wrote: >> >>> Send Connotea-code-devel mailing list submissions to >>> con...@li... >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> https://lists.sourceforge.net/lists/listinfo/connotea-code-devel >>> or, via email, send a message with subject or body 'help' to >>> con...@li... >>> >>> You can reach the person managing the list at >>> con...@li... >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of Connotea-code-devel digest..." >>> >>> >>> Today's Topics: >>> >>> 1. development questions (Andrew Su) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Mon, 25 Jun 2007 10:39:14 -0700 >>> From: "Andrew Su" <as...@gn...> >>> Subject: [Connotea-code-devel] development questions >>> To: <con...@li...> >>> Message-ID: >>> <190...@EX...> >>> Content-Type: text/plain; charset="us-ascii" >>> >>> Hello, >>> >>> >>> >>> I've been lurking on both the connotea mailing lists for a while now and >>> I thought I'd pose a basic question... Is there a public plan for >>> future connotea development? I think it's great that the code is open >>> source, but it appears that coding is still being primarily done by >>> Nature and NeoReality folks (not sure if the latest enhancements are >>> posted to sourceforge though). Is there a desire to open up the >>> development team to include other developers who want to see connotea >>> mature faster? I've been helping to explore thesis project ideas for a >>> couple bioinformatics masters students, and collaborating on connotea >>> may be an interesting prospect. >>> >>> >>> >>> And on another note, does anyone have a good feeling for the reasons why >>> connotea is not being used more? Of course, I'm asking this question >>> not knowing anything about usage statistics, only that I don't know >>> anyone personally (myself included) that uses it in production. My >>> reason? What someone referred to as Buggotea >>> (http://www.nodalpoint.org/2007/03/30/so_connotea_or_citeulike), which >>> really hinders the social aspect of the site. >>> >>> >>> >>> Any thoughts appreciated... >>> >>> >>> >>> Cheers, >>> >>> -andrew >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> >>> ------------------------------ >>> >>> ------------------------------------------------------------------------- >>> This SF.net email is sponsored by DB2 Express >>> Download DB2 Express C - the FREE version of DB2 express and take >>> control of your XML. No limits. Just data. Click to get it now. >>> http://sourceforge.net/powerbar/db2/ >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> Connotea-code-devel mailing list >>> Con...@li... >>> https://lists.sourceforge.net/lists/listinfo/connotea-code-devel >>> >>> >>> End of Connotea-code-devel Digest, Vol 14, Issue 14 >>> *************************************************** >> > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Connotea-code-devel mailing list > Con...@li... > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel |
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From: John-Paul R. <jp...@ua...> - 2007-06-26 13:20:04
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I've been a lurker for a while too and have enjoyed this thread and update. I currently use connotea-code for an internal bookmarking service. I just wanted to put a vote in for more project transparency. I'm interested in contributing to a modification to support the use of webiso for authnz (Shibboleth to be specific) so that it can be integrated with our local collaboration environment. ~jpr Mulvany, Ian wrote: > Hi Andrew, > > I'll start with your last point first. We will be resolving the buggotea > problem for articles that have identifiers, be those PMID's or DOI's. We use > an MD5 hash of the URI of a resource as the key identifier in the MySQL db > for each bookmark, and the way the code is written at the moment makes it a > very difficult task to change this, but we will be able to at least > pseudo-merge resources that have the identifiers mentioned. > > The first part of your post is very interesting. You are right about the > development taking place mostly between NPG and Neo-reality. There was a > slow-down in development at the beginning of this year as we had a change > over in people. I've joined NPG to work on Connotea, and have been writing > up a plan for it's development. I'm really keen to encourage as much > participation as I can. We have moved the live Connotea Code into a Darcs > repository to simplify distributed development and we should be releasing a > new OS release within a few weeks. > > I think you idea of opening up the plan is also a very good one, and I will > put up on the Connotea Wiki what we will be planning to do and when, along > with what we would like to do, but possibly don't have time for, when I have > the plan finalised. > > - Ian > > > On 25/6/07 20:05, "con...@li..." > <con...@li...> wrote: > >> Send Connotea-code-devel mailing list submissions to >> con...@li... >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/connotea-code-devel >> or, via email, send a message with subject or body 'help' to >> con...@li... >> >> You can reach the person managing the list at >> con...@li... >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Connotea-code-devel digest..." >> >> >> Today's Topics: >> >> 1. development questions (Andrew Su) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Mon, 25 Jun 2007 10:39:14 -0700 >> From: "Andrew Su" <as...@gn...> >> Subject: [Connotea-code-devel] development questions >> To: <con...@li...> >> Message-ID: >> <190...@EX...> >> Content-Type: text/plain; charset="us-ascii" >> >> Hello, >> >> >> >> I've been lurking on both the connotea mailing lists for a while now and >> I thought I'd pose a basic question... Is there a public plan for >> future connotea development? I think it's great that the code is open >> source, but it appears that coding is still being primarily done by >> Nature and NeoReality folks (not sure if the latest enhancements are >> posted to sourceforge though). Is there a desire to open up the >> development team to include other developers who want to see connotea >> mature faster? I've been helping to explore thesis project ideas for a >> couple bioinformatics masters students, and collaborating on connotea >> may be an interesting prospect. >> >> >> >> And on another note, does anyone have a good feeling for the reasons why >> connotea is not being used more? Of course, I'm asking this question >> not knowing anything about usage statistics, only that I don't know >> anyone personally (myself included) that uses it in production. My >> reason? What someone referred to as Buggotea >> (http://www.nodalpoint.org/2007/03/30/so_connotea_or_citeulike), which >> really hinders the social aspect of the site. >> >> >> >> Any thoughts appreciated... >> >> >> >> Cheers, >> >> -andrew >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> >> ------------------------------ >> >> _______________________________________________ >> Connotea-code-devel mailing list >> Con...@li... >> https://lists.sourceforge.net/lists/listinfo/connotea-code-devel >> >> >> End of Connotea-code-devel Digest, Vol 14, Issue 14 >> *************************************************** > > |
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From: Mulvany, I. <i.m...@na...> - 2007-06-26 09:58:14
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Hi Andrew, I'll start with your last point first. We will be resolving the buggotea problem for articles that have identifiers, be those PMID's or DOI's. We use an MD5 hash of the URI of a resource as the key identifier in the MySQL db for each bookmark, and the way the code is written at the moment makes it a very difficult task to change this, but we will be able to at least pseudo-merge resources that have the identifiers mentioned. The first part of your post is very interesting. You are right about the development taking place mostly between NPG and Neo-reality. There was a slow-down in development at the beginning of this year as we had a change over in people. I've joined NPG to work on Connotea, and have been writing up a plan for it's development. I'm really keen to encourage as much participation as I can. We have moved the live Connotea Code into a Darcs repository to simplify distributed development and we should be releasing a new OS release within a few weeks. I think you idea of opening up the plan is also a very good one, and I will put up on the Connotea Wiki what we will be planning to do and when, along with what we would like to do, but possibly don't have time for, when I have the plan finalised. - Ian On 25/6/07 20:05, "con...@li..." <con...@li...> wrote: > Send Connotea-code-devel mailing list submissions to > con...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel > or, via email, send a message with subject or body 'help' to > con...@li... > > You can reach the person managing the list at > con...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Connotea-code-devel digest..." > > > Today's Topics: > > 1. development questions (Andrew Su) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 25 Jun 2007 10:39:14 -0700 > From: "Andrew Su" <as...@gn...> > Subject: [Connotea-code-devel] development questions > To: <con...@li...> > Message-ID: > <190...@EX...> > Content-Type: text/plain; charset="us-ascii" > > Hello, > > > > I've been lurking on both the connotea mailing lists for a while now and > I thought I'd pose a basic question... Is there a public plan for > future connotea development? I think it's great that the code is open > source, but it appears that coding is still being primarily done by > Nature and NeoReality folks (not sure if the latest enhancements are > posted to sourceforge though). Is there a desire to open up the > development team to include other developers who want to see connotea > mature faster? I've been helping to explore thesis project ideas for a > couple bioinformatics masters students, and collaborating on connotea > may be an interesting prospect. > > > > And on another note, does anyone have a good feeling for the reasons why > connotea is not being used more? Of course, I'm asking this question > not knowing anything about usage statistics, only that I don't know > anyone personally (myself included) that uses it in production. My > reason? What someone referred to as Buggotea > (http://www.nodalpoint.org/2007/03/30/so_connotea_or_citeulike), which > really hinders the social aspect of the site. > > > > Any thoughts appreciated... > > > > Cheers, > > -andrew > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > > ------------------------------ > > _______________________________________________ > Connotea-code-devel mailing list > Con...@li... > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel > > > End of Connotea-code-devel Digest, Vol 14, Issue 14 > *************************************************** -- Ian Mulvany i.m...@na... +44(0)2078434756 www.nature.com www.connotea.org -- ******************************************************************************** DISCLAIMER: This e-mail is confidential and should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage mechanism. Neither Macmillan Publishers Limited nor any of its agents accept liability for any statements made which are clearly the sender's own and not expressly made on behalf of Macmillan Publishers Limited or one of its agents. Please note that neither Macmillan Publishers Limited nor any of its agents accept any responsibility for viruses that may be contained in this e-mail or its attachments and it is your responsibility to scan the e-mail and attachments (if any). No contracts may be concluded on behalf of Macmillan Publishers Limited or its agents by means of e-mail communication. Macmillan Publishers Limited Registered in England and Wales with registered number 785998 Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS ******************************************************************************** |
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From: Martin F. <ma...@ne...> - 2007-06-25 23:41:32
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Hi Andrew, Your point about the weighting of articles in regards to the multi-URI problem is well taken. > Yeah, I saw the Web API and think it's obviously very cool. Very Web2.0, mashup-friendly, etc. But having said that, I see the tools utilizing the Web API (http://www.connotea.org/wiki/ConnoteaTools) as bells and whistles, while there are still some meaty things to be done with the core application. For example, how many of the feature requests (http://www.connotea.org/wiki/RequestedFeatures) or bug reports (http://www.connotea.org/wiki/PossibleProblems) could/should be addressed through the web API? (Not a rhetorical question...) Well, no, not many of those ones. But to be fair the requested features list probably errs on the side of listing everything that could be done and not just what *will* be done (but then also partly because priorities change and we might change our mind and come back to it). > Obviously it's easy for the peanut gallery to inundate you with suggestions from the outside. But my question boils down to this -- is there a structure (and a desire by current developers) by which outside developers can aid the effort? Specifically on issues which you (current developers) or we (bioinformatics community) deem to be critical? To answer your question literally, the list here is the best form of organization for outside developers to initiate offers to build things, and we certainly set it up in the hopes of attracting outside participation. Unfortunately the formal bug tracker software is private (Nature internal). Ian Mulvany is the manager at Nature that sets our priorities and I'm sure he will have something to say on this general issue. If you or your students were to work on a sizable project, which wasn't just for your own purposes (i.e. for a local codebase running your own site), then it would make sense for Ian to be involved in helping you select the task, and then me to be involved in engineering decisions. We'd be excited for masters students to do thesis projects with Connotea or Connotea Code - if the only deciding factor was that we needed a bit more public structure, then I think you will find us interested in the suggestions. Martin |
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From: Andrew S. <as...@gn...> - 2007-06-25 22:59:28
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Martin, Thanks for your informative reply. Clearly lots of information. Let me = cherry-pick two points for a follow-up. > I agree that evangelism is necessary, and Connotea probably can't be a > del.icio.us or digg.com because it strives to serve scientists, so > unless the "anyone" in your sentence consists of scientists I would = not > expect it to hold a high percentage of users. Yeah, my mental calculations had already normalized for the size of the = scientific community... ;) But agreed on all your points (that many = users do use it despite current limitations, that scientists in general = are slow to the social bookmarking bandwagon, etc.). So then I = especially agree with you that evangelism is an important piece of = getting the word out (and hence increasing the value of the = application). In science, there is no higher evangelism than a = scientific publication, so what is the plan there? I think a scientific = publication that demonstrates the incredible value of social bookmarking = in the scientific literature would go a long way to introducing people = to the concept and building a user base. =20 But what is needed to demonstrate scientific value? I think an = important piece of that is actually the multi-URI bookmarks. Suppose, = for example, I stumble on a gene that I haven't studied before ('akt' = for example) and I want to get up to speed as quickly as possible. If I = search 'akt' in connotea, I get back 215 references, the vast majority = of which were only tagged by a single user. So this is good in that it = tells me that *someone* found these articles useful (a far cry less than = the 13218 from Pubmed), but still not as useful as non-scientific = searches at delicious, where the number of tags is a rough estimate of = importance. But at least part of the problem is the multi-URI issue. = If within that list of 215 references, you text search for "Rhinovirus = Activates Interleukin-8 Expression...", you see that both sundog and = saumen tagged this article. As a connotea user, I would like to = highlight this article as having twice the importance of most, but = connotea doesn't recognize that they are the same article. In summary, I sort of view connotea now as an online bookmarking system, = but not quite yet a social bookmarking system. And in my na=EFve view, = I think solving the multi-URI issue will lead to better = importance-by-voting, in turn leading to more scientific value, leading = to a bigger community, leading to better importance-by-voting, ... And, = of course, a cool publication in there would help jump-start things too. > What I suggest to anyone looking to get interested with Connotea Code = is > to look first at the well-demarcated points in the code - the Web API, > which is external and lets you talk to connotea.org from the language = of > your choice, and internally in the main Perl code, the citation source > module "API" and the import module "API", which are points in the > codebase where it was deliberately intended that programmers from > different groups would contribute. Something in that realm would be an > ideal test project to get you started. Yeah, I saw the Web API and think it's obviously very cool. Very = Web2.0, mashup-friendly, etc. But having said that, I see the tools = utilizing the Web API (http://www.connotea.org/wiki/ConnoteaTools) as = bells and whistles, while there are still some meaty things to be done = with the core application. For example, how many of the feature = requests (http://www.connotea.org/wiki/RequestedFeatures) or bug reports = (http://www.connotea.org/wiki/PossibleProblems) could/should be = addressed through the web API? (Not a rhetorical question...) Obviously it's easy for the peanut gallery to inundate you with = suggestions from the outside. But my question boils down to this -- is = there a structure (and a desire by current developers) by which outside = developers can aid the effort? Specifically on issues which you = (current developers) or we (bioinformatics community) deem to be = critical? Cheers, -andrew |
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From: Martin F. <ma...@ne...> - 2007-06-25 21:01:52
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Hi Andrew, Thanks for posting two great questions. Andrew Su wrote: > I’ve been lurking on both the connotea mailing lists for a while now and > I thought I’d pose a basic question… Is there a public plan for future > connotea development? I think it’s great that the code is open source, > but it appears that coding is still being primarily done by Nature and > NeoReality folks (not sure if the latest enhancements are posted to > sourceforge though). Is there a desire to open up the development team > to include other developers who want to see connotea mature faster? > I’ve been helping to explore thesis project ideas for a couple > bioinformatics masters students, and collaborating on connotea may be an > interesting prospect. I'd say if you look over the majority of open source projects, the participation of outsiders beyond the original founding members is always a bit thin, and even in some successful projects consists mostly of infrequent bursts of work to produce specific patches rather than bona fide ongoing development. So it's not uncommon. Add to that the fact that Connotea Code is not small and requires understanding of a handful of dependencies like mod_perl and memcached. I'm still optimistic that Connotea Code can and will pick up some outside contributions to the core code, but I suspect they will come from academic institutions (as you allude). I'm happy to say we've just successfully dumped CVS in favour of Darcs and that is working out great. This, I think, strategically supports coder participation, because Darcs is one of the new generation of *distributed* version control systems. What we're working on now is cleaning up our internal repository with the goal of having an open source release soon and toying with the idea of making the Darcs repository public to make it less necessary to make official releases. What I suggest to anyone looking to get interested with Connotea Code is to look first at the well-demarcated points in the code - the Web API, which is external and lets you talk to connotea.org from the language of your choice, and internally in the main Perl code, the citation source module "API" and the import module "API", which are points in the codebase where it was deliberately intended that programmers from different groups would contribute. Something in that realm would be an ideal test project to get you started. > And on another note, does anyone have a good feeling for the reasons why > connotea is not being used more? Of course, I’m asking this question > not knowing anything about usage statistics, only that I don’t know > anyone personally (myself included) that uses it in production. My > reason? What someone referred to as Buggotea > (http://www.nodalpoint.org/2007/03/30/so_connotea_or_citeulike), which > really hinders the social aspect of the site. Ian and I just spoke on the phone a couple hours ago about this. It is now high on our priority list. The merits of multi-URI bookmarks notwithstanding, I'm not sure it actually detracts from the number of users of Connotea; it doesn't feel like a big enough reason. Are you perhaps muddling the concept of who might have not heard of Connotea yet (or even the social bookmarking phenomenon in general) with who might have tried Connotea and chosen to leave it because of a specific property of the service? I agree that evangelism is necessary, and Connotea probably can't be a del.icio.us or digg.com because it strives to serve scientists, so unless the "anyone" in your sentence consists of scientists I would not expect it to hold a high percentage of users. As for people not liking some property of the service, we do know about a couple issues (and the issue you mention is one of them), but if I may offer you a countering anecdotal report, it only seems to be on the radar of a minority percentage of our users and even then not enough to abandon the service if they otherwise like it. If I may make a heretical observation ;-) some people do try social bookmarking and then sort of lose interest as well. I'd suggest this group is larger than those who leave because of, say, the URI-centric issue. Social bookmarking is an interesting development of technology that like everything else will take a few years to flourish and has to go through the normal growth phase. (Or am I wrong?) Cheers, Martin |
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From: Andrew S. <as...@gn...> - 2007-06-25 17:39:26
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Hello, =20 I've been lurking on both the connotea mailing lists for a while now and I thought I'd pose a basic question... Is there a public plan for future connotea development? I think it's great that the code is open source, but it appears that coding is still being primarily done by Nature and NeoReality folks (not sure if the latest enhancements are posted to sourceforge though). Is there a desire to open up the development team to include other developers who want to see connotea mature faster? I've been helping to explore thesis project ideas for a couple bioinformatics masters students, and collaborating on connotea may be an interesting prospect. =20 =20 And on another note, does anyone have a good feeling for the reasons why connotea is not being used more? Of course, I'm asking this question not knowing anything about usage statistics, only that I don't know anyone personally (myself included) that uses it in production. My reason? What someone referred to as Buggotea (http://www.nodalpoint.org/2007/03/30/so_connotea_or_citeulike), which really hinders the social aspect of the site. =20 =20 Any thoughts appreciated... =20 Cheers, -andrew |
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From: Mulvany, I. <i.m...@na...> - 2007-06-15 09:32:10
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Hi Rich, We are aware of the throttling issue and have been discussing some solutions that would allow us to stop having to throttle these requests. I don't know exactly what we are going to do about the situation yet, but we have a number of options on the table. I believe that we will have a solution within the next couple of months. Thanks for letting us know that the suggested fix doesn't seem to be working for you. We will look into that. Cheers, - Ian On 14/6/07 20:14, "con...@li..." <con...@li...> wrote: > Send Connotea-code-devel mailing list submissions to > con...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel > or, via email, send a message with subject or body 'help' to > con...@li... > > You can reach the person managing the list at > con...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Connotea-code-devel digest..." > > > Today's Topics: > > 1. Un-throttling API requests (richard apodaca) > 2. Re: Un-throttling API requests (Noel O'Boyle) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Jun 2007 16:50:11 -0700 (PDT) > From: richard apodaca <ric...@ya...> > Subject: [Connotea-code-devel] Un-throttling API requests > To: con...@li... > Message-ID: <866...@we...> > Content-Type: text/plain; charset=iso-8859-1 > > Newb here. I noticed that throttling of API requests > was recently discussed: > > http://sourceforge.net/mailarchive/message.php?msg_id=a882e48b0705310128k7aabb > cf6m464bd00c0908f03b%40mail.gmail.com > > and also: > > http://www.connotea.org/wiki/Throttling > > I've also experienced what Noel is describing - after > about 5 rapid-succession GETs I get 503 errors. Then > after about 5 seconds without issuing GETs, API > requests are processed. > > There was a suggestion to set WWW::Connotea as the > user agent to fix the problem. I'm using the Ruby API > which apparently does this by setting: > > AGENT = 'WWW::Connotea (ruby net/http)' > > This doesn't seem to do the trick, though. Is there > really a way to 'unthrottle' API requests and if so > how? > > I also like Noel's suggestion to accept more complex > queries as a way to avoid the throttling issue. > > thanks, > Rich > > ____________________________ > Richard Apodaca > Blog: http://depth-first.com > > > > ______________________________________________________________________________ > ______ > Get your own web address. > Have a HUGE year through Yahoo! Small Business. > http://smallbusiness.yahoo.com/domains/?p=BESTDEAL > > > > ------------------------------ > > Message: 2 > Date: Thu, 14 Jun 2007 08:11:46 +0100 > From: "Noel O'Boyle" <bao...@gm...> > Subject: Re: [Connotea-code-devel] Un-throttling API requests > To: "richard apodaca" <ric...@ya...> > Cc: con...@li... > Message-ID: > <a88...@ma...> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > I must admit that the suggestion didn't work for me either, but in the > end I just released my code anyway, with a 2 second interval between > API calls. > Noel > > On 14/06/07, richard apodaca <ric...@ya...> wrote: >> Newb here. I noticed that throttling of API requests >> was recently discussed: >> >> http://sourceforge.net/mailarchive/message.php?msg_id=a882e48b0705310128k7aab >> bcf6m464bd00c0908f03b%40mail.gmail.com >> >> and also: >> >> http://www.connotea.org/wiki/Throttling >> >> I've also experienced what Noel is describing - after >> about 5 rapid-succession GETs I get 503 errors. Then >> after about 5 seconds without issuing GETs, API >> requests are processed. >> >> There was a suggestion to set WWW::Connotea as the >> user agent to fix the problem. I'm using the Ruby API >> which apparently does this by setting: >> >> AGENT = 'WWW::Connotea (ruby net/http)' >> >> This doesn't seem to do the trick, though. Is there >> really a way to 'unthrottle' API requests and if so >> how? >> >> I also like Noel's suggestion to accept more complex >> queries as a way to avoid the throttling issue. >> >> thanks, >> Rich >> >> ____________________________ >> Richard Apodaca >> Blog: http://depth-first.com >> >> >> >> _____________________________________________________________________________ >> _______ >> Get your own web address. >> Have a HUGE year through Yahoo! Small Business. >> http://smallbusiness.yahoo.com/domains/?p=BESTDEAL >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> Connotea-code-devel mailing list >> Con...@li... >> https://lists.sourceforge.net/lists/listinfo/connotea-code-devel >> > > > > ------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > > ------------------------------ > > _______________________________________________ > Connotea-code-devel mailing list > Con...@li... > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel > > > End of Connotea-code-devel Digest, Vol 14, Issue 9 > ************************************************** ******************************************************************************** DISCLAIMER: This e-mail is confidential and should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage mechanism. Neither Macmillan Publishers Limited nor any of its agents accept liability for any statements made which are clearly the sender's own and not expressly made on behalf of Macmillan Publishers Limited or one of its agents. Please note that neither Macmillan Publishers Limited nor any of its agents accept any responsibility for viruses that may be contained in this e-mail or its attachments and it is your responsibility to scan the e-mail and attachments (if any). No contracts may be concluded on behalf of Macmillan Publishers Limited or its agents by means of e-mail communication. Macmillan Publishers Limited Registered in England and Wales with registered number 785998 Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS ******************************************************************************** |
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From: Noel O'B. <bao...@gm...> - 2007-06-14 07:11:52
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I must admit that the suggestion didn't work for me either, but in the end I just released my code anyway, with a 2 second interval between API calls. Noel On 14/06/07, richard apodaca <ric...@ya...> wrote: > Newb here. I noticed that throttling of API requests > was recently discussed: > > http://sourceforge.net/mailarchive/message.php?msg_id=a882e48b0705310128k7aabbcf6m464bd00c0908f03b%40mail.gmail.com > > and also: > > http://www.connotea.org/wiki/Throttling > > I've also experienced what Noel is describing - after > about 5 rapid-succession GETs I get 503 errors. Then > after about 5 seconds without issuing GETs, API > requests are processed. > > There was a suggestion to set WWW::Connotea as the > user agent to fix the problem. I'm using the Ruby API > which apparently does this by setting: > > AGENT = 'WWW::Connotea (ruby net/http)' > > This doesn't seem to do the trick, though. Is there > really a way to 'unthrottle' API requests and if so > how? > > I also like Noel's suggestion to accept more complex > queries as a way to avoid the throttling issue. > > thanks, > Rich > > ____________________________ > Richard Apodaca > Blog: http://depth-first.com > > > > ____________________________________________________________________________________ > Get your own web address. > Have a HUGE year through Yahoo! Small Business. > http://smallbusiness.yahoo.com/domains/?p=BESTDEAL > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Connotea-code-devel mailing list > Con...@li... > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel > |
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From: richard a. <ric...@ya...> - 2007-06-13 23:50:21
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Newb here. I noticed that throttling of API requests was recently discussed: http://sourceforge.net/mailarchive/message.php?msg_id=a882e48b0705310128k7aabbcf6m464bd00c0908f03b%40mail.gmail.com and also: http://www.connotea.org/wiki/Throttling I've also experienced what Noel is describing - after about 5 rapid-succession GETs I get 503 errors. Then after about 5 seconds without issuing GETs, API requests are processed. There was a suggestion to set WWW::Connotea as the user agent to fix the problem. I'm using the Ruby API which apparently does this by setting: AGENT = 'WWW::Connotea (ruby net/http)' This doesn't seem to do the trick, though. Is there really a way to 'unthrottle' API requests and if so how? I also like Noel's suggestion to accept more complex queries as a way to avoid the throttling issue. thanks, Rich ____________________________ Richard Apodaca Blog: http://depth-first.com ____________________________________________________________________________________ Get your own web address. Have a HUGE year through Yahoo! Small Business. http://smallbusiness.yahoo.com/domains/?p=BESTDEAL |
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From: Mulvany, I. <i.m...@na...> - 2007-06-13 14:56:45
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Hi Aaron, As far as I know no one has done this yet. - Ian On 12/6/07 20:08, "con...@li..." <con...@li...> wrote: > Send Connotea-code-devel mailing list submissions to > con...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel > or, via email, send a message with subject or body 'help' to > con...@li... > > You can reach the person managing the list at > con...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Connotea-code-devel digest..." > > > Today's Topics: > > 1. JavaScript to import information from Connotea (Aaron Rester) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 12 Jun 2007 14:05:16 -0500 > From: Aaron Rester <ar...@uc...> > Subject: [Connotea-code-devel] JavaScript to import information from > Connotea > To: con...@li... > Message-ID: <813...@uc...> > Content-Type: text/plain; charset="us-ascii" > > Hello, > > My apologies if this is not the proper venue in which to ask this > question, but I am wondering if anyone has written a JavaScript to > import information from a Connotea group in another webpage. I looked > at the API information page, but I'm not a programmer so it made > little sense to me. > > Thanks in advance for your help, > Aaron > > -- > Aaron Rester > Communications Coordinator > Center for International Studies > University of Chicago > Pick Hall 122 > 5828 S. University Ave., Chicago, IL 60637 > office phone: (773) 702-1743 > cell phone: (773) 680-2834 > e-mail: ar...@uc... > http://internationalstudies.uchicago.edu > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > > ------------------------------ > > _______________________________________________ > Connotea-code-devel mailing list > Con...@li... > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel > > > End of Connotea-code-devel Digest, Vol 14, Issue 7 > ************************************************** -- Ian Mulvany i.m...@na... +44(0)2078434756 www.nature.com www.connotea.org -- ******************************************************************************** DISCLAIMER: This e-mail is confidential and should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage mechanism. Neither Macmillan Publishers Limited nor any of its agents accept liability for any statements made which are clearly the sender's own and not expressly made on behalf of Macmillan Publishers Limited or one of its agents. Please note that neither Macmillan Publishers Limited nor any of its agents accept any responsibility for viruses that may be contained in this e-mail or its attachments and it is your responsibility to scan the e-mail and attachments (if any). No contracts may be concluded on behalf of Macmillan Publishers Limited or its agents by means of e-mail communication. Macmillan Publishers Limited Registered in England and Wales with registered number 785998 Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS ******************************************************************************** |
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From: Aaron R. <ar...@uc...> - 2007-06-12 19:05:33
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Hello, My apologies if this is not the proper venue in which to ask this question, but I am wondering if anyone has written a JavaScript to import information from a Connotea group in another webpage. I looked at the API information page, but I'm not a programmer so it made little sense to me. Thanks in advance for your help, Aaron -- Aaron Rester Communications Coordinator Center for International Studies University of Chicago Pick Hall 122 5828 S. University Ave., Chicago, IL 60637 office phone: (773) 702-1743 cell phone: (773) 680-2834 e-mail: ar...@uc... http://internationalstudies.uchicago.edu |
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