can you updated the server so that the most recent articles can be found?
发自网易邮箱大师 在2017年07月25日 11:49，Yaoqi Zhou 写道： Fast searching of articles related to your PubMed indexed paper Are you spending too much time searching the literature to prepare your grant proposals, manuscripts and keeping track of research happening in your field? We have built a literature-based search engine (http://pubmed.ict.griffith.edu.au/) which is powered by a combination of state-of-the-art methods to locate relevant articles to your published PubMed-indexed papers within a few seconds. While providing you the ability to locate relevant articles, we are seeking your feedback regarding the performance of these algorithms. By annotating recommended articles as relevant, somewhat relevant, or irrelevant, you are participating in a community-wide effort of establishing a gold-standard benchmark for relevant literature search. The accuracy of this benchmark is ensured by your domain knowledge and experience as your judgements will be based in the context of your own article. With your expertise, the entire process will take only a few minutes to complete (1 paper, 6 recommendations). Upon completion, this community-wide dataset will be available to freely download and redistribute, encouraging development of next-generation literature searching and retrieval methodologies, something we all desperately need. Due to current data availability, this relevant-paper search is limited to papers indexed by PubMed between January 1, 2007 to December 31, 2016 (the end of last year). Click http://pubmed.ict.griffith.edu.au/ to start. As this is a product in development, any constructive comments and suggestions will be truly appreciated. If you like this idea of community-wide benchmark for literature recommendation, please forward this email to your colleagues in the scientific community. Initial feedbacks to our server. “The process was certainly fast!”, “Although the articles found in the search were not necessarily exactly relevant, many are articles that I don't think I would have come across easily with a traditional search”, “Very nice work. I think there can be a longer list” (limited to 30 currently). Thank you! Yaoqi Professor Yaoqi Zhou | Research Leader Institute for Glycomics Griffith University | Gold Coast campus | QLD 4222 | Institute for Glycomics (G24) Room 2.10 T +61 7 5552 8228 | F +61 7 5552 9040 | email yaoqi.z...@griffith.edu.au http://sparks-lab.org (Group webpage) http://griffith.edu.au/institute-glycomics (Institute Webpage) On 25 Jul 2017, at 9:01 AM, CCP4BB automatic digest system <lists...@jiscmail.ac.uk> wrote: There are 14 messages totaling 9878 lines in this issue. Topics of the day: 1. Buccaneer places residues in different asymmetric units (3) 2. Primer design (7) 3. PhD position at University of Oslo 4. Postdoctoral position at Boston Children’s Hospital 5. About weighting factor settings in new ccp4i2 (2) ---------------------------------------------------------------------- Date: Mon, 24 Jul 2017 16:56:51 +0800 From: Lingxiao Zeng <lxz...@connect.hku.hk> Subject: Buccaneer places residues in different asymmetric units Dear All, I tried to use buccaneer to build a model. The starting model is a partial model, after model building the Rwork and Rfree are reasonable but buccaneer places residues in different asymmetric units and the model looks really weird. Is there any way to build the model into the same ASU or put different parts together after model building? Thanks! Best, Alice -- Lingxiao Zeng PhD candidate School of Biomedical Sciences The University of Hong Kong ------------------------------ Date: Mon, 24 Jul 2017 10:35:17 +0100 From: Jon Agirre <jon.agi...@york.ac.uk> Subject: Re: Buccaneer places residues in different asymmetric units Dear Alice, there's an option in both ccp4i and ccp4i2 interfaces that lets you tell Buccaneer that you want to build the new model in the same place as the partial model supplied - see my screenshots for reference. It might not be on by default and perhaps it should be. Please be aware that most newer developments and improvements will be put on the ccp4i2 interface to Buccaneer - it would be helpful if you could have a go and let us know what you think! Hope this helps, Jon On 24 July 2017 at 09:56, Lingxiao Zeng <lxz...@connect.hku.hk> wrote: Dear All, I tried to use buccaneer to build a model. The starting model is a partial model, after model building the Rwork and Rfree are reasonable but buccaneer places residues in different asymmetric units and the model looks really weird. Is there any way to build the model into the same ASU or put different parts together after model building? Thanks! Best, Alice -- Lingxiao Zeng PhD candidate School of Biomedical Sciences The University of Hong Kong -- Dr Jon Agirre York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, England http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ Twitter: @alwaysonthejazz +44 (0) 1904 32 8270 ------------------------------ Date: Mon, 24 Jul 2017 11:26:00 +0000 From: syed ibrahim <b_syed_ibra...@yahoo.com> Subject: Primer design Hello All I am interested in cloning a gene from a plant. I searched the database only partial sequence is available, ie: for 160 residues only. The full length of the protein is around 570 residues. I designed forward primer and I have no clue to design reverse primer. Any help Thank you Syed ------------------------------ Date: Mon, 24 Jul 2017 07:41:15 -0400 From: Artem Evdokimov <artem.evdoki...@gmail.com> Subject: Re: Primer design Have to do primer walking in a cdna library first. Artem On Jul 24, 2017 7:26 AM, "syed ibrahim" < 0000048c02cac012-dmarc-requ...@jiscmail.ac.uk> wrote: Hello All I am interested in cloning a gene from a plant. I searched the database only partial sequence is available, ie: for 160 residues only. The full length of the protein is around 570 residues. I designed forward primer and I have no clue to design reverse primer. Any help Thank you Syed ------------------------------ Date: Mon, 24 Jul 2017 17:12:39 +0530 From: Debasish Kumar Ghosh <dkgh...@cdfd.org.in> Subject: Re: Primer design Dear Syed, The process is very trivial to clone your gene of interest. Assuming your gene is transcribed as mono-cistronic mRNA, take the oligodT primer as reverse primer. First isolate the total RNA from the tissue or cells and do the cDNA synthesis using oligodT primer followed by gene specific PCR with forward primer and oligodT primer from the cDNA pool. Sequence the PCR product to get to know the first stop codon in the ORF. Making the specific reverse primer from the sequence is then just matter of time. Hope this helps. Best wishes, Debasish CSIR- Senior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html ----- Original Message ----- From: "syed ibrahim" <0000048c02cac012-dmarc-requ...@jiscmail.ac.uk> To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, July 24, 2017 4:56:00 PM Subject: [ccp4bb] Primer design Hello All I am interested in cloning a gene from a plant. I searched the database only partial sequence is available, ie: for 160 residues only. The full length of the protein is around 570 residues. I designed forward primer and I have no clue to design reverse primer. Any help Thank you Syed ------------------------------ Date: Mon, 24 Jul 2017 13:22:03 +0100 From: Eleanor Dodson <eleanor.dod...@york.ac.uk> Subject: Re: Buccaneer places residues in different asymmetric units Or use PISA to position bits sensibly.. Eleanor On 24 July 2017 at 10:35, Jon Agirre <jon.agi...@york.ac.uk> wrote: Dear Alice, there's an option in both ccp4i and ccp4i2 interfaces that lets you tell Buccaneer that you want to build the new model in the same place as the partial model supplied - see my screenshots for reference. It might not be on by default and perhaps it should be. Please be aware that most newer developments and improvements will be put on the ccp4i2 interface to Buccaneer - it would be helpful if you could have a go and let us know what you think! Hope this helps, Jon On 24 July 2017 at 09:56, Lingxiao Zeng <lxz...@connect.hku.hk> wrote: Dear All, I tried to use buccaneer to build a model. The starting model is a partial model, after model building the Rwork and Rfree are reasonable but buccaneer places residues in different asymmetric units and the model looks really weird. Is there any way to build the model into the same ASU or put different parts together after model building? Thanks! Best, Alice -- Lingxiao Zeng PhD candidate School of Biomedical Sciences The University of Hong Kong -- Dr Jon Agirre York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, England http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ Twitter: @alwaysonthejazz +44 (0) 1904 32 8270 ------------------------------ Date: Mon, 24 Jul 2017 13:18:25 +0000 From: "Keller, Jacob" <kell...@janelia.hhmi.org> Subject: Re: Primer design ....Or sequence the whole exome for what, $500-1000? JPK -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Debasish Kumar Ghosh Sent: Monday, July 24, 2017 7:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Primer design Dear Syed, The process is very trivial to clone your gene of interest. Assuming your gene is transcribed as mono-cistronic mRNA, take the oligodT primer as reverse primer. First isolate the total RNA from the tissue or cells and do the cDNA synthesis using oligodT primer followed by gene specific PCR with forward primer and oligodT primer from the cDNA pool. Sequence the PCR product to get to know the first stop codon in the ORF. Making the specific reverse primer from the sequence is then just matter of time. Hope this helps. Best wishes, Debasish CSIR- Senior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html ----- Original Message ----- From: "syed ibrahim" <0000048c02cac012-dmarc-requ...@jiscmail.ac.uk> To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, July 24, 2017 4:56:00 PM Subject: [ccp4bb] Primer design Hello All I am interested in cloning a gene from a plant. I searched the database only partial sequence is available, ie: for 160 residues only. The full length of the protein is around 570 residues. I designed forward primer and I have no clue to design reverse primer. Any help Thank you Syed ------------------------------ Date: Mon, 24 Jul 2017 19:02:19 +0530 From: Debasish Kumar Ghosh <dkgh...@cdfd.org.in> Subject: Re: Primer design No need of the whole exome. Sequencing The second PCR product will do the job I guess. Second PCR (from the cDNA pool) with specific forward primer and and oligodA reverse primer. Surely a matter of less than $3 Best, DKG ----- Original Message ----- From: "Jacob Keller" <kell...@janelia.hhmi.org> To: "Debasish Kumar Ghosh" <dkgh...@cdfd.org.in>, CCP4BB@JISCMAIL.AC.UK Sent: Monday, July 24, 2017 6:48:25 PM Subject: RE: Primer design ....Or sequence the whole exome for what, $500-1000? JPK -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Debasish Kumar Ghosh Sent: Monday, July 24, 2017 7:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Primer design Dear Syed, The process is very trivial to clone your gene of interest. Assuming your gene is transcribed as mono-cistronic mRNA, take the oligodT primer as reverse primer. First isolate the total RNA from the tissue or cells and do the cDNA synthesis using oligodT primer followed by gene specific PCR with forward primer and oligodA primer from the cDNA pool. Sequence the PCR product to get to know the first stop codon in the ORF. Making the specific reverse primer from the sequence is then just matter of time. Hope this helps. Best wishes, Debasish CSIR- Senior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html ----- Original Message ----- From: "syed ibrahim" <0000048c02cac012-dmarc-requ...@jiscmail.ac.uk> To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, July 24, 2017 4:56:00 PM Subject: [ccp4bb] Primer design Hello All I am interested in cloning a gene from a plant. I searched the database only partial sequence is available, ie: for 160 residues only. The full length of the protein is around 570 residues. I designed forward primer and I have no clue to design reverse primer. Any help Thank you Syed ------------------------------ Date: Mon, 24 Jul 2017 15:33:29 +0000 From: Kaare Bjerregaard-Andersen <kaare.bjerregaard-ander...@kjemi.uio.no> Subject: PhD position at University of Oslo Dear all, a PhD student position is now available at the Department of Chemistry, University of Oslo, Norway. Please find the announcement attached. The project focuses on the implementation of neutron based methods in the study of a surface-active bacterial colonization factor and is supervised by Prof. Ute Krengel and Assoc. Prof. Reidar Lund. Application deadline is 1st of september. Link to the position: https://www.jobbnorge.no/ledige-stillinger/stilling/140728/phd-research-fellow-in-structural-biology-and-soft-matter-technologies? best Kaare Bjerregaard-Andersen -- Kaare Bjerregaard-Andersen, M.Sc., Ph.D. Post-doctoral researcher Ute Krengel group Department of Chemistry University of Oslo P.O.Box 1137 Blindern 0318 Oslo, Norway phone +47 92553589 email kaar...@kjemi.uio.no ------------------------------ Date: Mon, 24 Jul 2017 15:43:15 +0000 From: "Keller, Jacob" <kell...@janelia.hhmi.org> Subject: Re: Primer design No need of the whole exome. Sequencing The second PCR product will do the job I guess. Second PCR (from the cDNA pool) with specific forward primer and and oligodA reverse primer. Surely a matter of less than $3 $3 is a major understimation, but I see your point. On the other hand, it is important to consider new technologies, and it would be a service to the scientific community to publish the exome somewhere, so other researchers would not have to spend their $3. JPK Best, DKG ----- Original Message ----- From: "Jacob Keller" <kell...@janelia.hhmi.org> To: "Debasish Kumar Ghosh" <dkgh...@cdfd.org.in>, CCP4BB@JISCMAIL.AC.UK Sent: Monday, July 24, 2017 6:48:25 PM Subject: RE: Primer design ....Or sequence the whole exome for what, $500-1000? JPK -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Debasish Kumar Ghosh Sent: Monday, July 24, 2017 7:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Primer design Dear Syed, The process is very trivial to clone your gene of interest. Assuming your gene is transcribed as mono-cistronic mRNA, take the oligodT primer as reverse primer. First isolate the total RNA from the tissue or cells and do the cDNA synthesis using oligodT primer followed by gene specific PCR with forward primer and oligodA primer from the cDNA pool. Sequence the PCR product to get to know the first stop codon in the ORF. Making the specific reverse primer from the sequence is then just matter of time. Hope this helps. Best wishes, Debasish CSIR- Senior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html ----- Original Message ----- From: "syed ibrahim" <0000048c02cac012-dmarc-requ...@jiscmail.ac.uk> To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, July 24, 2017 4:56:00 PM Subject: [ccp4bb] Primer design Hello All I am interested in cloning a gene from a plant. I searched the database only partial sequence is available, ie: for 160 residues only. The full length of the protein is around 570 residues. I designed forward primer and I have no clue to design reverse primer. Any help Thank you Syed ------------------------------ Date: Mon, 24 Jul 2017 13:27:12 -0400 From: Bing Chen <bc...@crystal.harvard.edu> Subject: Postdoctoral position at Boston Children’s Hospital A postdoctoral position is available immediately in Dr. Bing Chen’s laboratory at Boston Children’s Hospital/Harvard Medical School. The ongoing projects include 1) biochemical and structural studies to elucidate molecular mechanisms of how HIV-1 enters host cells, 2) design and production of HIV-1 envelope-based immunogens, and 3) development of antiviral therapeutics. For our recent publications, please see: Cai et al., Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):4477-4482. (https://www.ncbi.nlm.nih.gov/pubmed/28396421 <https://www.ncbi.nlm.nih.gov/pubmed/26113642>) Dev et al., Science. 2016 Jul 8;353(6295):172-5. (https://www.ncbi.nlm.nih.gov/pubmed/27338706 <https://www.ncbi.nlm.nih.gov/pubmed/27338706>) Chen et al., Science. 2015 Jul 10;349(6244):191-5. (https://www.ncbi.nlm.nih.gov/pubmed/26113642 <https://www.ncbi.nlm.nih.gov/pubmed/26113642>) A strong background in protein biochemistry and/or structural biology is required. We are particularly interested in those who are highly motivated and willing to tackle difficult problems. Applicants should send a cover letter, CV, and contact information of three references to Bing Chen (bc...@crystal.harvard.edu <mailto:bc...@crystal.harvard.edu>). ------------------------------ Date: Mon, 24 Jul 2017 20:44:45 +0000 From: Tom Peat <tom.p...@csiro.au> Subject: Re: Primer design A lot of plant genomes are big- wheat for example is 12 Gb, so it may not be quite as trivial as one might expect. cheers, tom Tom Peat Proteins Group Biomedical Program, CSIRO 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au ________________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Keller, Jacob <kell...@janelia.hhmi.org> Sent: Tuesday, July 25, 2017 1:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Primer design No need of the whole exome. Sequencing The second PCR product will do the job I guess. Second PCR (from the cDNA pool) with specific forward primer and and oligodA reverse primer. Surely a matter of less than $3 $3 is a major understimation, but I see your point. On the other hand, it is important to consider new technologies, and it would be a service to the scientific community to publish the exome somewhere, so other researchers would not have to spend their $3. JPK Best, DKG ----- Original Message ----- From: "Jacob Keller" <kell...@janelia.hhmi.org> To: "Debasish Kumar Ghosh" <dkgh...@cdfd.org.in>, CCP4BB@JISCMAIL.AC.UK Sent: Monday, July 24, 2017 6:48:25 PM Subject: RE: Primer design ....Or sequence the whole exome for what, $500-1000? JPK -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Debasish Kumar Ghosh Sent: Monday, July 24, 2017 7:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Primer design Dear Syed, The process is very trivial to clone your gene of interest. Assuming your gene is transcribed as mono-cistronic mRNA, take the oligodT primer as reverse primer. First isolate the total RNA from the tissue or cells and do the cDNA synthesis using oligodT primer followed by gene specific PCR with forward primer and oligodA primer from the cDNA pool. Sequence the PCR product to get to know the first stop codon in the ORF. Making the specific reverse primer from the sequence is then just matter of time. Hope this helps. Best wishes, Debasish CSIR- Senior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html ----- Original Message ----- From: "syed ibrahim" <0000048c02cac012-dmarc-requ...@jiscmail.ac.uk> To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, July 24, 2017 4:56:00 PM Subject: [ccp4bb] Primer design Hello All I am interested in cloning a gene from a plant. I searched the database only partial sequence is available, ie: for 160 residues only. The full length of the protein is around 570 residues. I designed forward primer and I have no clue to design reverse primer. Any help Thank you Syed ------------------------------ Date: Mon, 24 Jul 2017 22:01:15 +0000 From: "Liu, Xu" <xu....@emory.edu> Subject: About weighting factor settings in new ccp4i2 Hi, In the new cpp4-7.0.042 (ccp4i2), where can I put in the weighting factor for B factor restrain weight (the ‘WBSKAL' setting) and/or x-ray terms relative to geometric restrains (the ‘MATRIX’ setting ) in refmac5? Basically I want to plug in those weighting factors from pdbredo into REFMAC5 for a few more refinement but cannot find in new ccp4. Thanks! ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ------------------------------ Date: Mon, 24 Jul 2017 23:41:57 +0100 From: Jon Agirre <jon.agi...@york.ac.uk> Subject: Re: About weighting factor settings in new ccp4i2 Dear Xu, you can input those keywords in the text box under 'Advanced options' in the 'refinement' task. Just make sure you click somewhere else after you're done putting the keywords in in order to have the text validated by the interface. Best regards, Jon On 24 July 2017 at 23:01, Liu, Xu <xu....@emory.edu> wrote: Hi, In the new cpp4-7.0.042 (ccp4i2), where can I put in the weighting factor for B factor restrain weight (the ‘WBSKAL' setting) and/or x-ray terms relative to geometric restrains (the ‘MATRIX’ setting ) in refmac5? Basically I want to plug in those weighting factors from pdbredo into REFMAC5 for a few more refinement but cannot find in new ccp4. Thanks! ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). -- Dr Jon Agirre York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, England http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ Twitter: @alwaysonthejazz +44 (0) 1904 32 8270 ------------------------------ End of CCP4BB Digest - 23 Jul 2017 to 24 Jul 2017 (#2017-205) *************************************************************
