If you didn't get a results update you can
recover hits from a certain time interval with the Quickstart+ feature at
http://pubcrawler.gen.tcd.ie/quickstart2.html.
Simply fill in your PubCrawler user name and password, the start and
end date to search for and click on 'Quickstart'.
Apologies for any inconvenience caused!
If you didn't get a results update you can either
wait for the next scheduled run or you can start your
queries manually with the Quickstart feature at
http://pubcrawler.gen.tcd.ie/quickstart.html.
Alternatively, you can log on to the main Web portal at
http://pubcrawler.gen.tcd.ie and then click the button
'Start queries!' near the top of the page.
Apologies for any inconvenience caused!
Update: We got hit by another power cut on Monday, 18th
December, and this time one of our servers didn't survive it. As of
today (Friday, 22nd December) the system is running fine and the
service should be back to normal.
To get the correct view of your results over that period,
please go to the Quickstart+ page at
http://pubcrawler.gen.tcd.ie/quickstart2.html
Fill in your PubCrawler user name and password,
specify all necessary e-mail and formating options,
insert a starting date and click on 'Quickstart'.
New results will be available in a short moment.
Apologies for any inconvenience caused!
Full functionality has now been restored and the next results will bring you up-to-date with the latest publications in your field of research.
In some cases notifications of new hits found on Monday could not be sent out in time, so please make sure to look for older hits in your results page, located at http://pubcrawler.gen.tcd.ie/db/username or accessible after login through the entry portal at http://pubcrawler.gen.tcd.ie
Apologies for any inconvenience caused!
If you didn't get a results update, you can either wait for the next scheduled run or you can start your queries manually with the Quickstart feature at http://pubcrawler.gen.tcd.ie/quickstart.html.
Alternatively, you can log on to the new web-interface at http://pubcrawler.gen.tcd.ie and then click the button 'Start queries!' near the top of the page.
Apologies for any inconvenience caused!
The reason for the update is the requirement by NCBI to use their E-Utilities for querying the databases. Incorporating newly retrieved results needs some formating and we used this opportunity to introduce a new output format that differs slightly from the NCBI look and feel, but is easier to maintain (i.e., more resistant to changes at NCBI). It also helps overcoming incompatibility problems with certain mail clients and avoidance of accidental classification as spam by allowing a more flexible choice of options for the mailed results. This will become fully usable with an update of the PubCrawler website, which is currently under development. You can try out a preliminary version at pubcrawler.gen.tcd.ie/index_new.html.
If you encounter any problems with the new output format (or the new website), please report them to pubcrawlerREMOVECAPShelp@gmail.com.
The malfunction of the GenBank queries has first been reported on August 16th (thanks to John and everybody else who mailed afterwards!). By default, PubCrawler only reports items that have been modified/inserted within the last 30 days. Unless you have changed the relentrezdate-option to 50 days (the next higher value) or more, you might miss out on some new entries. To retrieve these, please use the Quickstart+ feature that allows you to carry out your searches on a specified data range (see PubCrawler FAQ, article 4b for more info).
Apologies for any inconvenience caused!
Apologies for any inconvenience caused!
Apologies for any inconvenience caused!
The new ones include 'Personal Name as Subject', 'Secondary Source ID', and 'Title/Abstract'.
Description for all search fields can be found at the PubMed help page: http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html#SearchFieldDescriptionsandTags
Please note that for compatibility reason the 'MEDLINE ID' field is still available, but it's use is deprecated because these identifiers are no longer assigned to PubMed citations. Please use PubMed ID's instead.
www.gen.tcd.ie/pubcrawler/...
should now be
pubcrawler.gen.tcd.ie/...
Results pages will still be accessible through the old links but everything else is automatically redirected to the new location.
Apologies for the lack of advanced warning, but these changes suddenly had to be rushed through.
If you notice any problems, please write an e-mail to pubcrawlerREMOVECAPShelp@gmail.com with a detailed description.
Just go to your PubCrawler results page at http://pubcrawler.gen.tcd.ie/db/username (or http://pubcrawler.gen.tcd.ie/cgi-bin/pubcrawler.results if 'Easy Check' is activated) and click on the 'Previous Results' button on the top right of the page. It will bring up a form in which you can specify a date range and start the immediate execution of your queries.
This is only a temporary hack and will be improved soon!
All the best for 2002 and Happy PubCrawling!
We will attempt to carry out all user jobs specifically scheduled for Sunday before that time.
The service should be back to normal on Monday.
Apologies for any inconvenience cause.
| p.s.: | Please remember that you can suspend your scheduled queries, which might be handy for the upcoming holiday season: http://pubcrawler.gen.tcd.ie/suspend_help.html |
At peak times connection to the server might be slow. If you can't access the website, please try again later.
As soon as circumstances allow it (probably within two to four weeks) the service will be back as usual. Please bear with us!
If you can't access the website, please try again later.
If your queries were not carried out or got stuck, please use Quickstart to start your PubCrawler jobs manually.
Apologies for any inconvenience this might cause!
Explanation: PubMed experienced some problem which resulted in the reports mentioned above. The faulty entries were withdrawn and will be added again in the future.
It's not certain that the same hits (with corrected journal names) will show up again in the PubCrawler results page. It is therefore recommended to check the 'x-day-old records'-links in your PubCrawler results until they come up with the proper entries.
Apologies for any inconvenience caused!
Update: http://www.nlm.nih.gov/pubs/techbull/jf01/jf01_technote.html#pubmed
(Thanks to Miriam for passing on this information!)
Update: The first chunk of new articles appeared: 6054 new articles added on 2001/02/07. These will all be automatically scanned by PubCrawler, given that your next searches will be carried out within the number of days specified by the 'relentrezdate' variable within your PubCrawler options (default: 30 days). If your queries are carried out at least once a week there should be no need to change your settings.
If you would like updates on your queries today, please use Quickstart to run your PubCrawler jobs manually.
Apologies for any inconvenience caused!
It's not certain if this feature will be available again in the future - we are awaiting information from NCBI regarding this. In the meantime we recommend to use the following tools for sequence updates:
- Peer Bork's lab at EMBL (BLAST sequence searches against DNA and protein databases)
- Swiss-Shop at Expasy (BLAST sequence and keyword searches against SwissProt updates)
If you have any problems to report, please write to pubcrawlerREMOVECAPShelp@gmail.com.
We regret any inconvenience caused by this!
Some data might be corrupted or lost. In that case try Quickstart to run your PubCrawler jobs manually. Also don't forget to check the links for hits from previous days.
If you have any problems to report, please write to pubcrawlerREMOVECAPShelp@gmail.com.
We are very sorry for any inconvenience caused by this!
The increasing number of queries that need to be carried out every day has brought the server very close to the limit of its memory capacity. After 120 days of uptime it will therefore shut down for the necessary work. The service will hopefully be back online one or two hours later.
The automated queries will not be affected by this!
The following table lists the email domains of our currently active users (= at least one query set up):
| # | DOM | Domain | Active Users | Percent | |
| 1 | EDU | US Educational | 944 | 18.8 % | |
| 2 | COM | US Commercial | 725 | 14.5 % | |
| 3 | NL | Netherlands | 480 | 9.6 % | |
| 4 | UK | United Kingdom | 465 | 9.3 % | |
| 5 | FR | France | 322 | 6.4 % | |
| 6 | CA | Canada | 314 | 6.3 % | |
| 7 | DE | Germany | 289 | 5.8 % | |
| 8 | IE | Ireland | 233 | 4.6 % | |
| 9 | AU | Australia | 159 | 3.2 % | |
| 10 | NET | Network | 96 | 1.9 % | |
| 11 | ORG | Non-Profit Organization | 94 | 1.9 % | |
| 12 | BE | Belgium | 92 | 1.8 % | |
| 13 | ES | Spain | 82 | 1.6 % | |
| 14 | JP | Japan | 81 | 1.6 % | |
| 15 | IT | Italy | 63 | 1.3 % | |
| 16 | DK | Denmark | 58 | 1.2 % | |
| 17 | GOV | US Government | 57 | 1.1 % | |
| 18 | other | 463 | 9.2 % | ||
| Total | 56 domains | 5017 users | |||
Sláinte!
The following table lists the email domains of our currently active users (= at least one query set up):
| DOM | Domain | Users | Percent | |
| 1 | EDU | US Educational | 790 | 19.6 % |
| 2 | COM | US Commercial | 542 | 13.5 % |
| 3 | NL | Netherlands | 396 | 9.8 % |
| 4 | UK | United Kingdom | 351 | 8.7 % |
| 5 | CA | Canada | 279 | 6.9 % |
| 6 | FR | France | 247 | 6.1 % |
| 7 | DE | Germany | 229 | 5.7 % |
| 8 | IE | Ireland | 218 | 5.4 % |
| 9 | AU | Australia | 95 | 2.4 % |
| 10 | NET | Network | 85 | 2.1 % |
| 11 | ORG | Non-Profit Organization | 79 | 2.0 % |
| 12 | JP | Japan | 66 | 1.6 % |
| 13 | BE | Belgium | 66 | 1.6 % |
| 14 | ES | Spain | 62 | 1.5 % |
| 15 | BR | Brazil | 50 | 1.2 % |
| 16 | IT | Italy | 48 | 1.2 % |
| 17 | NO | Norway | 44 | 1.1 % |
| 18 | other | 375 | 9.3 % | |
| Total | 55 domains | 4022 users | ||
Sláinte!
- A patch was applied to PubCrawler which undecodes the ampersand sign (&) in hypertext links.
Thanks very much to Dmitry Mozzherin from BioMail for the hint!
- A new option for the emailed results is available:
In the slim HTML page general NCBI links and tables are filtered out.
Please modify your settings (following the according button from the top of your results page) if you like to change the format of results emailed to you.
Many users whose queries were executed on Friday (24/03/00) and Saturday (25/03/00) will therefore find a huge increase in hits which include a lot of backdated reports.
We have changed PubCrawler's internals again to deal with this problem. It's currently running normal - until the next surprise from NCBI!
You can filter out all the old hits from your results by starting your queries again manually:
- go to PubCrawler's Quickstart
- fill in your username and password
- click the 'Quickstart'-button
- follow the link to your results page
- click the refresh/reload button of that browser and continue with that until searches are terminated
However, if you prefer to get emails every time your searches are carried out, then you have to change your settings accordingly:
- go to your results page ( http://pubcrawler.gen.tcd.ie/db/user_name )
- click on the button labeled 'Modify Settings'
- you will reach a page with all your settings (either directly or after password dialog)
- find a green box starting with 'Do you wish to get emails....'
- click the button beside 'send mail every time'
- fill in your password and click on 'Change Data'
| Check out older news as well! |
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