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The [HSPH Bioinformatics Core](https://hsphbio.ghost.io/) (HBC) — through funding from the [HMS Tools and Technology Program](http://hms.harvard.edu/departments/tools-and-technology) (TnT) and the [Harvard NeuroDiscovery Center](http://www.neurodiscovery.harvard.edu/) (HNDC) — provides a single point of contact for Harvard Medical School researchers interested in bioinformatics support.
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Core staff aid researchers within the Harvard community with the **management, integration and contextual analysis of biological high-throughput data**, focusing on **next-generation sequencing support**. We [provide consulting, training, tools, databases and best practices](#services), foster collaboration and a community of bioinformatics activities, and build a unified infrastructure supporting a diverse set of experimental systems and high-throughput biological data.
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With the help of this funding HBC can now **offer subsidized [consults](#fees)** to researchers with a primary affiliation in one of the [Basic and Social Science Departments on the Quad](http://hms.harvard.edu/departments) or any affiliation with the HNDC. Please [contact us](#contact) with any questions and support requests you might have.
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title: About
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# Bioinformatics Support for HMS
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The [HSPH Bioinformatics Core](https://hsphbio.ghost.io/) (HBC) provides bioinformatics support for Harvard Medical School researchers. This has been made possible through funding from the [HMS Tools and Technology Program](http://hms.harvard.edu/departments/tools-and-technology) (TnT) and the [Harvard NeuroDiscovery Center](http://www.neurodiscovery.harvard.edu/) (HNDC).
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Our Core staff are available to help with the **management, integration, and contextual analysis of high-throughput biological data**, focusing on **next-generation sequencing support**. We [provide consulting, training, tools, databases and best practices](#services), foster collaboration and a community of bioinformatics activities, and are building unified infrastructure to support a diverse set of experimental systems and high-throughput biological data.
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With the help of this funding, HBC can now **offer subsidized [consults](#fees)** to researchers with a primary affiliation in one of the [Basic and Social Science Departments on the Quad](http://hms.harvard.edu/departments) or any affiliation with the HNDC. Please [contact us](#contact) with any questions and support requests you might have.
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We follow **best practices** and re-use public workflows and tools wherever possible, but are happy to adapt existing methods and develop new solutions where required. We can **support grant proposals on short notice**. The Core’s team has extensive experience in providing standard descriptions for data management, user and security handling, quality controls and data dissemination that fulfill NIH and NSF requirements and simplify the process of finishing your grant or manuscript.
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While we can offer support in most areas of computational biology HBC’s expertise is **focused on three key domains**:
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While we can offer support in most areas of computational biology, HBC’s expertise are **focused on four key domains**:
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### 1. Next generation sequencing analysis:
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Core analysts have extensive experience in [managing and analyzing sequencing data](https://bcbio-nextgen.readthedocs.org/), including whole genome and exome sequencing (quality control, mapping, re-alignment, variant calls, prioritization), RNA-seq (quantification and _de novo_ transcriptome analysis), genome assembly (reference guided and _de novo_) and epigenomics. We can also provide support in the design and and analysis of your customized NGS experiment.
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Core analysts have extensive experience in [managing and analyzing sequencing data](https://bcbio-nextgen.readthedocs.org/), including whole genome and exome sequencing (quality control, mapping, re-alignment, variant calls, prioritization), RNA-seq (quantification and _de novo_ transcriptome analysis), genome assembly (reference guided and _de novo_) and epigenomics. We can also provide support in the design and and analysis of your customized NGS experiment. We follow **best practices** and re-use public workflows and tools wherever possible, but are happy to adapt existing methods and develop new solutions where required.
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### 2. Functional analysis:
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We can provide a path from genes to function by delivering extensive functional annotation, prioritizing new markers and developing testable hypotheses for future experiments. We test for functional information using different gene set enrichment approaches (using Gene Ontology, pathway databases as well as curated and generic gene sets), provide context by integrating your data with public resources such as [GEO](http://www.ncbi.nlm.nih.gov/geo/) and [ArrayExpress](http://www.ebi.ac.uk/arrayexpress/), and explore the biological interaction space in co-expression and high-throughput interaction data sets using network analysis techniques.
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We can provide a path from genes to function by delivering extensive functional annotation, prioritizing new markers, and developing testable hypotheses for future experiments. We test for functional information using different gene set enrichment approaches (using Gene Ontology, pathway databases, and curated and generic gene sets), provide context by integrating your data with public resources such as [GEO](http://www.ncbi.nlm.nih.gov/geo/) and [ArrayExpress](http://www.ebi.ac.uk/arrayexpress/), and explore the biological interaction space in co-expression and high-throughput interaction data sets using network analysis techniques.
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### 3. Research computing support:
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Due to our collaboration with the [Harvard Medical School Research Computing Group](https://rc.hms.harvard.edu/) team we can also help with more general problems of computational infrastructure to optimally support your project, including data storage, backup, server setup and access to [Orchestra](https://rc.hms.harvard.edu/#orchestra), a high performance cluster. Where needed we can also work with you to run large scale analysis on [Amazon’s AWS](https://aws.amazon.com/) (Cloud) environment.
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Our collaboration with the [HMS Research Computing](https://rc.hms.harvard.edu/) team means that we can also help with more general problems of computational infrastructure to optimally support your project, including data storage, backup, server setup, and access to [Orchestra](https://rc.hms.harvard.edu/#orchestra), a high performance cluster. Where needed we can also work with you to run large scale analysis on [Amazon’s AWS](https://aws.amazon.com/) (Cloud) environment.
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### 4. Grant support:
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We can **support grant proposals on short notice**. The Core’s team has extensive experience in providing standard descriptions for data management, user and security handling, quality controls, and data dissemination that fulfill NIH and NSF requirements and simplify the process of finishing your grant or manuscript.
HBC works as a **recharge center**. Consults are billed at **$125/hour** after an initial meeting to discuss your project. This model ensures that we can flexibly assign the right combination of expertise to your specific tasks. We will provide you with a estimate of the number of hours required, a quote and a start date as part of our [Memorandum of Understanding](https://dl.dropboxusercontent.com/u/407047/Ghost/hbc/CHB%20MOU.pdf) (PDF). During the project you will receive detailed monthly billing updates and ongoing analysis results via our project page.
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**Fees** for pilot projects, grant-writing related data analysis and other short term consults **can be subsidized** in many cases through support from the [HMS Tools and Technology Program](http://hms.harvard.edu/departments/tools-and-technology) and funding from the [Harvard NeuroDiscovery Center](http://www.neurodiscovery.harvard.edu/). If in doubt [ask us for more information](#contact)!
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title: Fees
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HBC works as a **recharge center**. Consults are billed at **$125/hour** after an initial meeting to discuss your project. This model ensures that we can flexibly assign the right combination of expertise to your specific tasks. We will provide you with a estimate of the number of hours required, a quote, and a start date as part of our [Memorandum of Understanding](https://dl.dropboxusercontent.com/u/407047/Ghost/hbc/CHB%20MOU.pdf) (PDF). During the project you will receive detailed monthly billing updates and ongoing analysis results via our project page.
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**Fees** for pilot projects, grant-writing related data analysis, and other short term consults **can be subsidized** in many cases through support from the [HMS Tools and Technology Program](http://hms.harvard.edu/departments/tools-and-technology) and funding from the [Harvard NeuroDiscovery Center](http://www.neurodiscovery.harvard.edu/). If in doubt [ask us for more information](#contact)!
You can send general enquiries and project requests via **[email](mailto:[email protected]) or phone (+1 617-365-0984)**. For administrative requests, please contact [Meagan Plante](mailto:[email protected]). Billing inquiries and grant-related questions are handled by [Rachel Boschetto](mailto:[email protected]). Alternatively, just stop by our office!
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We are located at the **Harvard School of Public Health, SPH2, 4th floor, Room 437A, 655 Huntington Ave**, Boston, MA 02115. Additional maps for the Longwood area, shuttle bus time tables and additional information can be found at the main [HSPH website](http://www.hsph.harvard.edu/about/location-and-directions/).
You can send general enquiries and project requests via **[email](mailto:[email protected]) or phone (+1 617-365-0984)**. For administrative requests, please contact [Meagan Plante](mailto:[email protected]). Billing inquiries and grant-related questions are handled by [Rachel Boschetto](mailto:[email protected]). Alternatively, just stop by our office!
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We are located at the **Harvard School of Public Health, SPH2, 4th floor, Room 437A, 655 Huntington Ave**, Boston, MA 02115. Additional maps for the Longwood area, shuttle bus time tables and additional information can be found at the main [HSPH website](http://www.hsph.harvard.edu/about/location-and-directions/).
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