Read full article on RAST German E. coli Strain Annotation Using Cloud Computing.

• Consistent annotations across all sequenced bacterial species from GenBank.

• Searches based on taxonomy, gene name, locus tag, protein function/families, pathways, EC numbers, GO terms, and more.

• Data and analysis results are free and typically downloadable.

• Organism summaries; pre-sorted PubMed articles; interactive phylogenetic trees; virulence and disease information, and experimental data including, transcriptomics, proteomics, protein structure, and protein-protein interactions.

• Numerous interactive visualizations for genome browsing, multi-genome comparisons, pathway comparisons, protein family comparisons, phylogenetic trees with coupled MSAs, 3D protein structures, and feature group comparisons.

Event includes free pizza dinner.  For registration information, agenda, and location details please see PATRIC VT Workshop Promo.

If you have a suggestion for a future workshop topic and/or location, please send it to us via the “contact us” link at the bottom of this page.

What PATRIC Offers:

• Consistent annotations across all sequenced bacterial species from GenBank.

• Searches based on taxonomy, gene name, locus tag, protein function/families, pathways, EC numbers, GO terms, and more.

• Data and analysis results are free and typically downloadable.

• Organism summaries; pre-sorted PubMed articles; interactive phylogenetic trees; virulence and disease information, and experimental data including, transcriptomics, proteomics, protein structure, and protein-protein interactions.

• Numerous interactive visualizations for genome browsing, multi-genome comparisons, pathway comparisons, protein family comparisons, phylogenetic trees with coupled MSAs, 3D protein structures, and feature group comparisons.

For registration information, agenda, and location please see Brucellosis Workshop Flyer.

If you have a suggestion for a future workshop topic and/or location, please send it to us via the “Contact Us” link at the bottom of this page.

A list of all proteins and their conformity scores is provided in an Excel file (ecoli9genocav).  Some of the proteins found in the outbreak strains have no homologs in E. coli.  In the conformity score column, these “unique” proteins are identified by a “-“.  The data for the unique proteins for all nine strains are also integrated into the PATRIC website, with the additional functionality the site provides (where applicable); you can access those data at the following links:

• LB226692 unique genes
• TY-2482 unique genes
• GOS1 unique genes
• GOS2 unique genes
• H112180280 unique genes
• H112180282 unique genes
• H112180283 unique genes
• H112180540 unique genes
• H112180541 unique genes

The divergent proteins (see above) were compared to virulence and antibiotic-resistance proteins collected from different sources with some interesting discoveries.  For example, beta-lactamase, a protein responsible for resistance to beta-lactam antibiotics like penicillins, cephamycins, and carbapenems was found to be identical in the nine outbreak strains (CTX-M type), but very different from their closest homologs prevalent in other E. coli strains (TEM-type).  An alignment of these proteins is shown here.  Other divergent proteins include ABC transporters, phage-related and outer-membrane proteins.

The proteins from the Escherichia coli strains TY-2482 and LB226692 were used to search a specific E. coli database (compiled with 184 E. coli genomes at PATRIC) using BLAST.  We calculated Smith-Waterman alignment scores for each of the top ten best-scoring homologs of these proteins and normalized the score to the self-alignment score, creating a conformity score.  Conformity scores of 1 mean that all proteins in the alignment are identical.  Proteins with conformity scores of 0.8 or less were considered to be “divergent” from their top ten homologs in E. coli.  A graphical representation, where conformity scores for over 5000 proteins of the E. coli strains TY-2482 and LB226692, is provided in the figure below. The X-axis is in log scale.

Click image to enlarge

A list of all proteins and their conformity scores is provided in an Excel file (TY2482-LB226692_Vir_ABR_Conformity_All).  Some of the proteins found in TY-2482 and LB226692 have no homologs in E. coli.  In the conformity score column, these “unique” proteins are identified by a “-“.  The data for the unique proteins for both species are also integrated into the PATRIC website here, with the additional functionality the site provides.

The divergent proteins (see above) were compared to virulence and antibiotic-resistance proteins collected from different sources with some interesting discoveries.  For example, beta-lactamase, a protein responsible for resistance to beta-lactam antibiotics like penicillins, cephamycins, and carbapenems was found to be identical in TY-2482 and LB226692 (CTX-M type), but very different from their closest homologs prevalent in other E. coli strains (TEM-type).  An alignment of these proteins is provided here.  Other divergent proteins include ABC transporters, phage-related and outermembrane proteins.

The two genomes have been annotated using RAST, making them consistent with the 184 E. coli genomes and the total 2,865 bacterial genomes available at PATRIC.  The proteins conserved across all E. coli have been used to generate a preliminary phylogenetic tree that is based on 166640 characters across 527 genes in 354 taxa.  This tree, shown below shows that the two new strains are most closely related to the pathogenic, enteroaggregative strain 559899.

Click Image to enlarge.

Click here to view this tree in its interactive form on the PATRIC Website.

The proteins from these two new pathogenic strains can be compared to other bacterial genomes using the PATRIC Protein Family Sorter.  An example of this, showing two of several unique islands that have been identified in these two genomes is provided in the figure below and in interactive form on the PATRIC Website by clicking here and then selecting the “Heatmap” tab.

See the Protein Family Sorter FAQs for help in using the sorter.  An Excel file with tabs containing lists of proteins in these islands is available by clicking E coli protein islands.

Click Image to enlarge.

For a comparison of the RAST annotations with the other publicized annotation click here.

Much of the information in PATRIC is updated on an ongoing basis.   Such as:

• Interactive Disease maps with outbreak information.  Click here and then select the Disease Map tab.
• The PATRIC Google news search for countermeasures and other information.  Click here.

Many laboratories are analyzing these genomes and providing data to the research community.  PATRIC is performing additional analyses, including collecting a list of the important genes identified, and will be providing gene trees and multiple sequence alignments of the genes with their closest homologs, which we will release as additional news items.  For updates:

• Check the PATRIC News Page.
• Follow us on Twitter.
• Follow us on Facebook.

For quarterly PATRIC updates on current PATRIC and PATRIC-related research, new PATRIC functionality, and PATRIC grant opportunities, please sign up for our PATRIC Newsletter.

QUESTIONS AND ANSWERS Updated October 28th. See bottom of this page.

The NIAID-funded Pathosystems Resource Integration Center (PATRIC) invites propos­als for Driving Biological Projects (DBPs) focused on one or more of the pathogens supported by this Bioinformatics Resource Center (BRC). We anticipate making a minimum of two awards of up to $600K each by April 1, 2012. A two page Letter of Intent (LOI) is due August 1, 2011. Full proposals will be solicited by invitation only, with a deadline of November 1, 2011.

DBP proposals must exploit high-throughput experimental technologies to functionally charac­terize bacterial species in order to help elucidate pathogenesis, antimicrobial resistance and/or other biological processes of interest in the study of bacterial infectious diseases.  Such approaches may incorporate expression profiling microarrays, proteomics studies, metabolomics, interactome analysis, RNAi experiments, RNA-Seq, Chip-Seq, bioassays, and/or other technologies.

All experimental results, data, metadata, and reagents generated by the DBPs must be released into the public domain, according to data release guidelines provided by PATRIC. NIAID man­dates that PATRIC staff assist with bioinformatics analysis and loading of data produced by the DBP, which may involve data management, computational and/or statistical analysis of experimental data, generating predictive models, developing algorithms for data analysis and visualization, etc.

Read further information about the BRC program on the NIAID website.

DBP Information

• Type of award: cost reimbursement subcontract.
• Number of awards: at least 2 (maximum total budget for all awards = $1.2M).
• Duration of each award: up to 24 months.
• Maximum budget per award: up to $600,000 in total costs.
• Letters of Intent must be submitted by 5:00 PM Eastern Time, August 1, 2011, via email to patric-dbp@vbi.vt.edu. LOIs are limited to 2 pages maximum, 11 pt font or larger.
• Full proposals will be solicited by invitation only, with a due date of 5:00 PM, Eastern Time, November 1, 2011, via email to patric-dbp@vbi.vt.edu. Full proposals are limited to 8 pages of text and figures (11 pt font or larger).  Biosketches and references are not included in the page count.  Appendices are discouraged.
• Projected start date: April 1, 2012.

Review

LOIs and Full Proposals will be reviewed by the BRC Scientific Working Group (SWG), an external board of advisors, based on the following criteria:

• Technical feasibility
• Scientific impact on the communities served by PATRIC
• Impact on the development of new features in PATRIC
• Cost-effectiveness

Recommendations from the SWG will be considered by PATRIC and NIAID program staff, which will be responsible for final selection of DBP awards.

Eligibility

All researchers with expertise and capabilities in the areas described above are invited to submit a Letter of Intent. DBP applicants / institutions need not be located in the US, but any local requirements must be compatible with NIH regulations and the tight time-lines noted above.  Members of the SWG are not precluded from submitting LOIs, but if selected to submit full appli­cations will not participate in the final review.  Per the PATRIC prime contract, the number of DBPs is limited to only one from the prime contractor’s and subcontractors’ institutions, including the DBPs’ institutions, during the entire contract period of performance.  Thus, proposals from institutions that have DBPs already awarded from PATRIC are ineligible.  Information about current PATRIC DBPs can be found here:

Letters of Intent

Submission of a Letter of Intent is required, via email to patric-dbp@vbi.vt.edu. The LOI must be no longer than 2 pages (11 pt font or larger), and must include the following components:

• PI name, affiliation and contact information
• Project title
• Pathogen(s) involved
• Project description including specific description of work proposed
• Explanation of how the project will utilize and complement BRC resources in expediting research on these pathogens by the larger scientific community

Projects considered competitive by the SWG and PATRIC staff in consultation with NIAID program officers will be invited to submit full proposals. Note that the SWG may suggest (but may not require) communication between applicants proposing similar projects in order to facil­itate coordination where appropriate.

Full Proposals – Only selected LOIs are eligible for Full Proposal submission

DBP proposals should be structured as a white paper, and must clearly address how the propos­ed project will exploit high-throughput experimental and bioinformatics techniques to functionally characterize the genome / proteome / metabolome of microbial species supported by PATRIC, helping to elucidate pathogenesis, antimicrobial resistance and/or other important infectious dis­ease processes. DBP proposals are limited to 8 pages of text and figures (11 pt font or larger), and must include the following information:

• Executive summary of the project’s goals, including the pathogen(s) involved, information to be produced, and the expected impact on scientific communities served by PATRIC.
• Description of the data to be produced, including methods used to generate this informa­tion and possible obstacles.  The proposal should also review any relevant datasets that are currently available, and discuss their relationship to the proposed project.  Projects involving animals and/or human subjects are subject to standard NIH regulations and must document relevant approvals.
• Details of high throughput experimental technologies necessary to carry out the project, noting currently available reagents, facilities, equipment and other resources.
• Discussion of computational and/or statistical analyses, noting those to be provided by the applicant, and those required from PATRIC (see below).
• Assessment of impact, including how these data are likely to influence development of new PATRIC features, and how they will be used by relevant research communities.
• Project timeline, including specific milestones and deliverables.
• Data release / data sharing plan, consistent with NIAID and BRC data release guidelines (see below).

Additional material to include in the proposal (not included in the 8 page limit):

• References
• List of proposed scientific and technical personnel, detailing qualifications, experience, and role(s) in the project. The DBP lead must devote at least 10% effort to this project.  Note: full CVs are not required.
• Proposed budget (maximum of $600K total costs over two years), broken down by category (labor, materials, other line items, as appropriate for the project). Note that cost effective­ness will be considered during review; budgets may be supplemented from other sources, and it is permissible to propose alternatives (e.g. line items detailing costs for pathogen A, pathogen B, dataset X, dataset Y, analysis N, etc). Use the NIH Budget and Budget Justification forms which can be downloaded from here: (Budget Justification Budget Template)

Please do not use appendices.

BRC Resource Utilization Plan: The proposal must include a specific plan that describes the intended PATRIC integration with the project and bioinformatics support expected from PATRIC. This section of the proposal must be submitted for review and evaluation at least one week before the proposal due date, submitted in MS Word format via email to patric-dbp@vbi.vt.edu. The response from PATRIC will either be “Yes, we can support what you are proposing”, or “No, we cannot support what you are proposing” with an indication of which part we will not be able to support and why. This information can be used by the proposer to modify their final proposal. At the time of final proposal submission PATRIC will provide an official letter that includes a description of the planned support from PATRIC that will be included with the proposal for SWG review.

Full Proposals are to be sent via email to: patric-dbp@vbi.vt.edu (contact rkenyon@vbi.vt.edu) if acknowledgement is not received within 72 hours of submission).  Proposals may be subject to further negotiation prior to acceptance, according to standard NIH subcontracting pro­cedures.  We anticipate notification of awards (or opening of further negotiations) on or about January 9, 2012, and that subcontract awards will be in place by March 1, 2012. The projected start date is April 1, 2012.

Data Release Policy

• All data and information generated under the DBP award must be made accessible to the PATRIC team immediately upon generation.
• Public release via the PATRIC Website is expected within one month from publication or within one year of generation, whichever comes first.
• Complete datasets, meta-data and reagents generated under the DBP award must also be made publicly available within the same time-frame, without restriction (e.g. MTA require­ments).  For example, sequences should be deposited in Genbank / EMBL / DDBJ, or the European Short Read Archive, as appropriate.  MIAME-compliant microarray data and MINSEQE-compliant RNA-Seq and ChIP-Seq data should be deposited at GEO / ArrayExpress / CIBEX, etc.  Reagents of general utility should be made available via the BEI, ATCC, or other appropriate distribution centers.
• Any exceptions to the above policies must be approved in writing by the PATRIC manage­ment and NIAID program officers.

Further information on data handling procedures and data management policies is posted on the PATRIC Website.

The NIAID will also review and provide the final approval of the DBPs proposed for award by the SWG. Final Proposals selected for submission to NIAID are subject to NIAID approval, NIAID supplemental award to the PATRIC prime contract, and successful subcontract negotiation between Virginia Tech and the potential awardee.

Questions and Answers

We will post questions received from submitters and our responses here on the PATRIC web site during the proposal preparation phase. If necessary, the question and answer will be re-phrased to make them generically relevant to all/other proposals.

Reporting Requirements

Semi-annual and periodic ad hoc reports will be required to assist with the review of progress toward stated goals.

We regret that it will not be possible to fund all of the valuable projects that one might envision in response to this solicitation, but look forward to continuing to work with the PATRIC user community to integrate additional datasets generated through other mech­anisms.  Click on the ʻContact Usʼ link at patric@vbi.vt.edu if you wish to discuss integration or bioinformatics support for datasets that are currently available or in preparation.

QUESTIONS AND ANSWERS Updated October 28th.
When will notifications go out about decisions on LOIs and invitations for full proposals?

We are targeting mid-September for notifications of decisions on LOIs.

What organisms are acceptable for study in the DBP?

The Driving Biological Project should focus on BACTERIAL pathogens that are the target of the PATRIC project, which include NIAID category A-C Priority Pathogens and Emerging and Re-Emerging Infectious Diseases.

• The target list of PATRIC pathogens can be found here: http://patricbrc.vbi.vt.edu/v0/organisms_we_study.html
• The complete NIAID Category A-C Pathogen list (all species) can be found here:
  http://www.niaid.nih.gov/topics/biodefenserelated/biodefense/research/pages/cata.aspx
• The complete NIAID Emerging and Re-Emerging Infectious Diseases list can be found here:
  http://www.niaid.nih.gov/topics/emerging/pages/list.aspx

Can an investigator on a current DBP apply to the new solicitation?

Our contract limits the number of DBPs from any single institution to only one.  However, it is permissible for an institution that currently has a DBP or investigator on one of the current DBPs to be part of a proposal for which a different institution will have the prime contract for the DBP.

Will DBPs support projects focused on the host side of host-pathogen interaction? That is, on projects aimed at identifying host regulatory and signaling pathways that 1) increase/decrease in response to infection and 2) contribute to host resistance or pathogen success.

DBP proposals must generate data to functionally charac­terize bacterial species in order to help elucidate pathogenesis, antimicrobial resistance and/or other biological processes of interest in the study of bacterial infectious diseases.  If the host data would be generated that results from interaction with the pathogen, we have means for using and supporting that data in PATRIC.

Can an interdisciplinary team of experimentalists and computational biologists apply to the DBP?  The solicitation emphasizes the analysis that the BRC team can provide to experimentalists?

It would be permissible for a team of experimentalists and computational biologists to apply.  It is important however that the DBP proposal describe how the BRC will be utilized during the course of the DBP.

Would your group be able to take raw transcriptomics (microarray and RNA-seq) and metabolic data and generate classifications based on levels of expression or metabolite concentrations?

Yes.

Would your group be able to help in modeling of metabolic pathways (flux) based on the data?

Yes.

After submitting the LOI when will we be notified whether we receive an invitation to write a full proposal?

Invitations for full proposals should go out in mid-September.

How many groups will be invited to submit full proposals?

There is no set number of full proposals we will solicit.  It will be driven by the quality & relevance of LOIs we receive.

Which institutions currently have a DBP?

Cornell University and University of California Irvine.  Details can be found here.

Is it more important to present the underlying biological question in the proposal or to elaborate on the technologies to be used, data to be generated, and use of PATRIC resources?

The proposal should be balanced in addressing the review criteria:

• Technical feasibility
• Scientific impact on the communities served by PATRIC
• Impact on the development of new features in PATRIC
• Cost-effectiveness

Thus, the biological question is relevant to the second criterion, and the use of PATRIC resources to the third.

Our DBP may focus on an organism studied under a current DBP.  Will this be a disadvantage?  Is there a preference for a wider coverage of organisms and data types?  Or are the underlying questions and approaches of greater significance?

The study of an organism currently covered by a DBP is not precluded nor necessarily disadvantaged, but justification that the questions and underlying approaches are more broadly applicable to other organisms would be helpful.

Does the BRC Resource Utilization Plan section of the proposal count against the 8-page limit, or is it considered additional material?  Is there a suggested length for this section?

The Utilization Plan does not count against the 8-page limit per se, but we ask that you include a 1-2 paragraph summary of the approved plan in your proposal.  The plan itself (due for review and evaluation at least one week before the proposal due date) can be whatever length you think is appropriate to describe how the interactions with the BRC will take place.  We expect that 1-2 pages would probably be sufficient.

Does the $600K total budget include indirect costs to the home institution?

Yes the $600K includes direct plus indirect costs.  The total amount of the budget cannot exceed $600K.

Our organization will be a subcontractor to the lead organization for the DBP.  What budget forms are required from our institution?

Use the templates found here:
http://www.patricbrc.org/patric/html/NIH_Budget_Template.Contract.xls
http://www.patricbrc.org/patric/html/NIH_Budget_Justification_Template.doc
NIH 2043 Form

What are features of the PATRIC  pipeline for RNA-Seq analyses?

At this point PATRIC doesn’t have any incorporated RNA-Seq tools.   However, by the proposed DBP start date 1-April-2012, we plan to have deployed a workflow that will allow a user to bring their RNA-Seq data, produce BAM and RPKM files, and filter and do analysis of results by visualizing that data in a private PATRIC context.  The planned PATRIC functionality includes the ability to view wiggle plots on the genome browser (along with other tracks), view and filter transcriptomic data, and view enrichment information.   Since part of the goal of the DBPs is to drive functionality at PATRIC, if you think features beyond this are desirable, they should be included as part of the proposal.  In the meantime, we have the ability and experience to process and help interpret RNA-Seq data.

Does PATRIC have tools for annotating ncRNAs?

PATRIC has in the past provided ncRNA annotations, but doesn’t currently provide such annotation in the PATRIC annotation system.   What you see at the PATRIC website are ncRNAs identified either in the RefSeq annotation or from earlier annotation systems.  This is something that we’d like to address but we don’t have a currently scheduled time frame for this feature.  If it is a requirement for your DBP, it would become a priority in PATRIC.

Does the NIH salary cap of $199,700 apply to the DBPs?

Yes, since PATRIC is NIH funded and the DBPs are part of that funding, the NIH salary cap applies.

Can the PATRIC team provide support for RNA-Seq data analysis for eukaryotic hosts.

Yes, the PATRIC team can provide support for RNA-Seq analysis of host as well as pathogen data.

Is there someone to talk with to get some more guidance about how to best write the full proposal?

Along with our NIAID Program Officer, we have decided that having individual conversations with DBP proposers could lead to the appearance of perhaps giving some proposals a competitive edge. Therefore we have decided that we will use email correspondences to answer specific questions and post generic forms of those questions and answers to the PATRIC website.

As for additional guidance, this is an NIH funded project and the reviewers are familiar with NIH formats and procedures. We suggest that you approach this as you would other NIH proposals, with particular attention to the required information.

Are letters of support permitted?

Yes, letters of support are permitted and they do not count against the 8-page limit.

Is an NIH biosketch needed in addition to the list of scientific and technical personnel?

No, you do not need to include an NIH biosketch in addition to the list of scientific and technical personnel.

What level of detail is required in the Materials and Supplies page of the budget?
The DBP awards will be via an NIH contract, so you should follow NIH Guidelines for contracts (not grants) in filling out the Materials and Supplies page in the budget.

My proposal is intended to generate data types or utilize analysis tools that I can’t find currently on the PATRIC website.  Is this a problem?
No, this is not a problem.  One of the review criteria for proposals is “Impact on the development of new features in PATRIC”  (see the other review criteria in the Review description above on this web page.)  The goal of this criterion is to drive the development of novel infrastructure that is generally usable by the community, and the idea is to develop it as part of collaboration with the DBP awardees that are generating the data and know how they want to utilize the data.

Where can we find the FAR clauses and other flow-down requirements that will apply to our subcontract, if selected for award?

The original RFA for the BRC program (of which PATRIC is one of the awardees) is below.  You should be able to find applicable terms and conditions there.  Note that we will be handling all of the information system requirements, so your institute should not have to be concerned with those.  If your institute is awarded one of the Driving Biological Projects, there will be an opportunity to negotiate terms and conditions as needed.

https://www.fbo.gov/spg/HHS/NIH/NIAID/NIH-NIAID-DMID-AI2008038/listing.html

Do I need to include anything other than the plan itself with respect to the BRC Utilization Plan in my application?

In the interest of time, we will forgo issuing a formal letter of approval from PATRIC.  The email approval will suffice, for which we have a copy, so you do not need to include anything else if you have received approval of the plan from us via email.

Will this project be funded by a NIH contract or grant?

PATRIC is a NIAID/NIH contract, and the DBP will be funded via subcontract from the PATRIC prime contract.

• Consistent annotations across all sequenced bacterial species from GenBank.

• Searches based on taxonomy, gene name, locus tag, protein function/families, pathways, EC numbers, GO terms, and more.

• Data and analysis results are free and typically downloadable.

• Organism summaries; pre-sorted PubMed articles; interactive phylogenetic trees; virulence and disease information, and experimental data including, transcriptomics, proteomics, protein structure, and protein-protein interactions.

• Numerous interactive visualizations for genome browsing, multi-genome comparisons, pathway comparisons, protein family comparisons, phylogenetic trees with coupled MSAs, 3D protein structures, and feature group comparisons.

Who Should Attend:

• Bacterial pathogen researchers/students and bioinformaticians.

For registration information, agenda, and location please see UC Davis Workshop Flyer.

• Consistent annotations across all sequenced bacterial species from GenBank.

• Searches based on taxonomy, gene name, locus tag, protein function/families, pathways, EC numbers, GO terms, and more.

• Data and analysis results are free and typically downloadable.

• Organism summaries; pre-sorted PubMed articles; interactive phylogenetic trees; virulence and disease information, and experimental data including, transcriptomics, proteomics, protein structure, and protein-protein interactions.

• Numerous interactive visualizations for genome browsing, multi-genome comparisons, pathway comparisons, protein family comparisons, phylogenetic trees with coupled MSAs, 3D protein structures, and feature group comparisons.

Who Should Attend:

• Bacterial pathogen researchers/students and bioinformaticians.

For registration information, agenda, and location please see OCICB Workshop Flyer.