© 2018 by Boston Childrens Hospital. 

 

Supporting Digital Science at Boston Children's Hospital

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The full menu of RC services

 

The page is a descriptive list of services provided by research computing, with links out to internal intranet pages as well as other external reference sites. Please note that many paragraphs on this page are complemented by additional information on our wiki: http://rcwiki. Once you familiarize yourself with the general services provided on this page, please bookmark the wiki and visit it often as the wiki pages are more dynamic. The wiki is meant to provide detailed information about our services. Any questions about the content of this page should be directed to research.computing@childrens.harvard.edu.

Please note, that in general, all clinical systems at BCH and centrally managed workstations are supported through the ISD Help Desk. The ISD Help Desk can also assist with password resets and network connectivity. You can contact them 24/day via the methods listed here.

 

Research Computing (RC) Help Desk provides more specialized support for individually managed research computers (desktops and laptops) and access to research software packages through Pediatric Scholar service.  In addition, RC Help Desk coordinates support for a wide range of scientific services, including  Genomics, Bioinformatics, Cohort Discovery, Electronic Data Capture, High-Performance Computing, Data Management, and Compliance with Research Computing Policies.

 

Descriptions of various research computing offerings are detailed below. The RC Help Desk can be reached by email at research.computing@childrens.harvard.edu and is attended during regular business hours.

 

Pediatric Scholar

 

Support for research computers is offered through Pediatric Scholar subscription. The service bundles a) remote as well as on-site technical support, b) access to 25+ commercial packages, 100+ Open Source applications, and c) Data Management Support. All members of the community can join the program, which is renewed on an annual basis. To enroll please visit the BCH intranet.

 

Relevant Web  and Intranet/Restricted (Pediatric Scholar Portal Links: enroll, request software), RC Support Portal (track your requests), BCH G Suite and ISD Help Desk.

 

A. Pediatric Scholar Support Services:

 

The RC Desktop Support Team is led by Joshua Lopez, who can assist with or expedite the services listed below. To schedule an informational appointment with Josh, and to inquire about our technical support services, available software, or to obtain more information about current projects please contact RC Help Desk at research.computing@childrens.harvard.edu.

 

  • Computer Registration: all users are required to register BCH computers and personal computers that are used on BCH premises. Contact RC Help Desk by email to start this process. At the time of the appointment we can also provide additional information about research computing support at BCH.

  • Remote Access: Junos Pulse Secure, the VPN client for Macs and PCs, can be downloaded from the BCH VPN webpage, and configured to connect to vpn.childrens.harvard.edu. Grid cards, which are required to establish connection can be picked-up from ISD at Fegan 014 during business hours. Web based VPN is also available and up-to-date instructions are availableRC Help Desk can assist with troubleshooting.

  • Email and Calendar: Pediatric Scholars should request Outlook 2016 and configure it with BCH credentials (user name format is: chboston.org\chXXXXXX). You can also access your email on the web.  BCH supplies a general email account and access to set your password and pin.  Access through other mail clients is not recommended and it is not supported.

  • Mailing Lists: Mailing lists with limited to BCH email accounts can be requested by writing to ISD Help Desk. Please include group name, which will be appended with -dl (distribution list) extension. Mailing lists addresses can be used to schedule appointments in outlook and can be expanded to see the full list of participants. RC Help Desk can help Pediatric Scholars to setup mailing lists that combine BCH and non-BCH email. A pediatric scholar will need to serve as a group administrator and will be responsible for message moderation and group membership.

  • Printers: Access to lab printers via print servers. Print servers are managed by several teams so it is best to contact RC Help Desk for instructions.

  • WiFi access: access to ‘TCH’ wireless networks is available at all on-campus locations. Please use your BCH login/password to authenticate. Keep in mind, your computer will need to be registered before it can properly connect to any BCH network.

  • Teleconferencing: Zoom is the approved BCH teleconferencing software. You can find info, guides, and request an account from internal eHelp site.

  • Phone: Phone support is provided by the Telecommunications ISD department and instructions to use Cisco phones are available online. In order to request a phone and active phone line, please email the ISD Help Desk. Please note, that RC Help Desk does not support phone systems.

  • Network Jack Activation: Connecting your devices via Ethernet will increase your internet connection speed. In order to request a port be activated, you can email or call the ISD Help Desk with the jack information written on the face plate (i.e. EN1-146/3). You can also work with RC Help Desk to fine-tune and troubleshoot connectivity issues.

  • Computer Support: RC Help Desk provides remote and on-site support. All Pediatric Scholars have access to this technical support, while others can easily enroll to obtain immediate access.

  • Computer purchases: RC Help Desk can advise with purchases of new systems. Standard configurations can be further customized to your individual needs.

  • Research Desktop Support (RDS) - data acquisition computers, shared computers, instrumentation computers: RC Help Desk can configure computers supporting lab equipment, backup data, optimize computer performance and configure separately licensed software. We also offer additional support options for shared computers and other types of on-premise and cloud computing resources.

 

B. Pediatric Scholar Software:

 

Many of the following titles are available through the self-service model and can be requested for immediate download through the Pediatric Scholar portal. The Portal provides detailed descriptions of available applications, and short descriptions of their use. Below we highlight some of the most commonly used packages.

For more information and immediate installation instructions please visit Pediatric Scholar portal.

 

  • Google G Suite: BCH G Suite My Drives and Team Drives currently have unlimited storage space. Google collaborative tools include Docs, Sheets, Forms, Slides and more that can be shared with collaborators. These tools allow users to, in real-time, collaborate on the creation of documents, spreadsheets, presentations with versioning and file recovery support (see also G Suite data management below).

  • Microsoft Office 2016: Scholars can request download of the newest standalone Microsoft Office applications, including MS Word, Excel, PowerPoint and Outlook, which can be installed on up to 5 devices. Access to Office requires that Research Computing add you to the license.

  • We also offer access to additional applications, including EndNote, the full Adobe Acrobat, ReadCube, Affinity Designer and Affinity Photo (Adobe Illustrator and Photoshop competitors).

  • Commercial Research software: Genomics, Bioinformatics, Statistics, Pathway Analysis software are described in the corresponding sections below.

  • Open Source Software: Access to 100+ Open Source applications are offered through BioGrid installer (Mac and Linux only). For the full list of applications please visit biogrids.org. Please note that all BioGrids applications are also available on HMS O2 cluster.

 

C. Pediatric Scholar Data Management:

 

Pediatric Scholar has several Data Management resources that are supported by Research Computing. RC provides consulting for data management plans, data storage options for both PHI and non-PHI, and computer backup solutions. Our technologies also cover general research needs such as lab notebooks and file sharing. Research Data Management is led by Kris Bolt who can work with investigators and labs to create custom data management plans and technical solutions that meet security requirements. To schedule an informational appointment with Kris, and for more information about our data management services, please contact the RC Help Desk at research.computing@childrens.harvard.edu.

 

Relevant Web  and Intranet/Restricted Links: Harvard Catalyst Data Planning ChecklistGoogle Team Drive Data ManagementRC-FS (Research Computing File Server)OAR (Online Access Request), internal knowledge base

 

Data Management, Storage and Backup:

  • Data Management and Compliance Consultation: For investigators navigating complex sponsor and BCH compliance requirements, Kris can assist by providing expertise and templates for data sharing or data management plan requirements.

    • A data management plan (DMP) is a written document describing the practices to be used throughout the data lifecycle. 

    • Research Computing can help you customize DMPs and review your draft DMP for sponsors, the IRB, and publisher requirements. The NIH has published general guidance on their DMP requirements, and we are creating a BCH guide that can be used to create a NIH-compliant DMP.  Many sponsors and publishers also now require data management or data sharing plans. ElsevierInternational Committee of Medical Journal EditorsNew England Journal of Medicine Publisher Requirements.

    •  In-person meetings are available to create custom data management or data sharing/publication plans for individual projects or lab best practices. Training on data management and/or compliance for labs or team drive members is also available on request by contacting the RC Help Desk.

  • LabArchives: Pediatric Scholars have access to cloud-based service for electronic lab notebooks that enables you to store, organize, and publish your research data. Interconnect lab data, manage files, observations and notes and easily import and access digital experimental data captured from lab machines. LabArchives stores all revisions by users for every entry for easy compliance with sponsor mandates to publish and share selected data or entire notebooks to specific individuals or the public.

  • Google G Suite: The new G Suite service offers a powerful array of collaborative and data management tools as well as productivity services. G Suite also includes unlimited storage space on My Drive and Team Drives to manage data sharing for any NON-PHI data. The current configuration of offerings is experimental, and changes may be made to the configurations as we pilot the program with investigators and team members.  If you are a Pediatric Scholar and would like to participate in a pilot, please contact us at the RC Help Desk.

  • DropBox: Pediatric Scholars have access to BCH DropBox accounts can accommodate 1TB+ of research data, and files can be shared with internal and external collaborators.

 

The following data management tools are available at an additional fee.  Please contact the RC Help Desk for more information.

  • RC-FS: File sharing: Research Computing supplies high-reliability file storage for labs, which is charged on a per-terabyte basis with one free TB for eligible researchers. We provide networked folders for both individual private use and collaborative use within a lab. Upon request, we provide limited-access folders within a share for more restricted work such as administrative files or project-specific data. Research Computing is able to facilitate collaboration and data exchange between different labs/divisions within the secure environment. Additionally, storage on RC-FS is backed up daily, weekly, and monthly to help prevent data loss. To request a new share please contact the RC Help Desk. If a team member needs access to a restricted lab folder, please use the OAR form.

  • Computer Backup: CrashPlan is our primary backup tool, used to protect user files and data on individually managed machine(s). It’s offered for MacOS, Windows and Linux computers. CrashPlan has flexible retention settings, compression methods and encryption that can be configured by the user across as many as four devices. CrashPlan also allows users to perform restores as desired, without the need for contacting RC. RC is available to assist with these actions upon request, if needed. Note that it is not designed to recover applications, settings or operating systems; these items are typically re-installed or configured after a system is rebuilt. If settings or application versions are critical to a system restore (typically seen in lab instruments), we advise additional conversation on an appropriate back up plan. Alternative backup services can be provided for enrolled assets in special cases. Contact the RC Help Desk for more information.

 

Research Computing Scientific Services  

 

Specialized scientific research services are provided by RC to all members of the BCH research community.  To inquire about any of these services please email the RC Help Desk.  

 

Genomics Data Commons:

 

The BCH Connect Genomics Data Commons leverages the WuXi NextCODE software suite to provide a centralized place for the deposition, storage and analysis of genomic data. The Genomic Data Commons exposes raw human exome data to rapid analysis, visualization and integration with information from public databases. Broadly consented data is queryable in the repository for matchmaking, additional analyses, cohort generation, and use as a control group. Researchers are invited to store and analyze their patients genomic and phenotypic data on this platform in a comparable, secure and accessible manner.

 

Shira Rockowitz, PhD, runs the RC Genomics and Bioinformatics team and can help you get data uploaded to the repository, advise on Mendelian and cohort analysis tools available through the platform, provide assistance with data interpretation and connect your group with additional resources. Shira also offers a popular Introductory Nanocourse on Genomic Analysis, during which all participants learn how to use the platform for Mendelian Analyses and start to look at tools to identify variation in genes across a cohort.

 

To schedule an informational appointment with Shira, sign up for a nanocourse, to inquire about analyzing data using WuXi NextCODE or other tools, please contact the RC Help Desk

 

Relevant Web  and Intranet/Restricted Links: Access WuXi NextCODESubmit DataBCH Connect OverviewStart Analyzing Data, MatchMaker, Getting Started Guides to: CSA, Sequence Miner, and GOR. Useful databases include: gnomADGTeXHuman Splicing FinderUCSC Genome BrowserVariation and TFBScBioPortal

 

Genomics Tools:

 

Shira Rockowitz, PhD, runs the RC Genomics and Bioinformatics team and can provide access to a wide variety of genomics tools, provide assistance with data interpretation and connect your group with additional external resources. We also coordinate the BCH 3000+ exome project, where data from sequencing vendors is integrated in BCH Connect system for further interpretation with WuXi NextCODE software (see Genomics Data Commons section above). Shira also offers a popular Introductory Nanocourse on Genomic Analysis.

 

To schedule an informational appointment with Shira, sign up for a research.computing@childrens.harvard.edu.nanocourse, to inquire about analyzing data using WuXi NextCODE or other tools, please contact the RC Help Desk at

 

Relevant Web  and Intranet/Restricted Links: Request SoftwareAccess WuXi NextCODE,  Submit DataBCH Connect OverviewStart Analyzing DataMatchMaker, Getting Started Guides to: CSA, Sequence Miner, and GOR, Getting Started with Golden Helix, Using Alamut, HGMD Getting Started Guide, Introduction to HGMD, Get Started with Geneious, IGV Tutorial, JMP Genomics Resources

 

Genomics Software available to Pediatric Scholars:

For more information and immediate installation instructions please visit Pediatric Scholar portal

  • BCH Connect Platform with WuXi NextCODE analysis: for rapid analysis and integration of raw human exome data files with information from public databases. The platform also simplifies the management, storage and sharing of genomic data.

  • Alamut Visual translates between coding regions and genomic loci for the interpretation of the effect of any human mutation; pools information from different splice prediction algorithms and conservation scores.

  • Human Gene Mutation Database (HGMD) contains 220,270 human gene mutations and disease associations, OMIM, PMID and notes for interpretation of variants; identifies publications that can be referenced to link variants with diseases and contribute evidence towards classification.

  • Geneious trims, assembles and visualizes Sanger sequencing files for variant confirmation and automatically adds annotations for any species. Geneious is a comprehensive bioinformatics and molecular biology tool (see Bioinformatics section below).

  • IGV, JMP Genomics, Pathway Analysis software (see Bioinformatics section below) and other applications are also available.

 

Bioinformatics Services:

 

We offer end-to-end services for individuals with all levels of bioinformatics expertise, including consulting, access to software packages and advice regarding the design and analysis of your bioinformatics experiments. Consulting support is coordinated by Shira Rockowitz, PhD, who can engage in-house and external bioinformatics experts.

 

Examples of projects that already converged successfully with our consulting support include CLIP-seq, single cell RNA-seq, CRISPR library screening and infrastructure projects including website redevelopment and international data systems. Additional types of projects that are supported include (but are not limited to):

  • transcriptomic analysis: (e.g. bulk RNA-seq, RNA modification sequencing analysis, non-coding RNA-seq, gene fusion analysis, transcriptome variation, alternative splicing)

  • whole exome / whole genome sequencing analyses: (genome assembly, variant calling, copy number variation)

  • microbiome and epigenomics analysis: (16S amplicon sequencing species identification, whole genome shotgun sequencing species identification, protein-DNA interactions: e.g., ChIP-seq peak analysis, methylome analysis: e.g., bisulfite sequencing analysis)

 

To schedule an informational appointment with Shira, to inquire about the cost of our partially-subsidized consulting service, or to obtain more information about completed projects, please contact RC Help Desk. Relevant Web  and Intranet/Restricted LinksRequest Software, Open Source Software provided by BioGrids Consortium, FlowJo Getting Started, Get Started with Geneious, IPA Quick Start, IPA Webinars, Cytoscape, MetaCore Training Materials: Training Manual, Advanced Training Manual and Example Analysis

 

Bioinformatics Software available to Pediatric Scholars:
For more information and immediate installation instructions please visit Pediatric Scholar portal

  • Geneious: The most recent addition to Pediatric Scholar, application Geneious provides one of the most comprehensive collection of molecular biology and NGS analysis tools, including tools to support RNA-seq analyses, tree building, cloning and more.

  • We also offer access to additional molecular biology applications, including DNASTAR Lasergene, MacVector and Sequencher.

  • FlowJo: analysis platform for single-cell flow cytometry data is widely used by BCH community. 

  • Pathway Analysis: several applications are available:

    • a) Ingenuity Pathway Analysis (IPA) supports searches for targeted information on genes, proteins, chemicals, and drugs;

    • b) Cytoscape provides a platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data;

    • c) MetaCore, which is available through HMS Countway Library, delivers high-quality biological systems content in context, giving researchers essential data and analytics to accelerate scientific research.

  • Open Source Software: Access to 100+ Open Source applications is offered through BioGrid installer (Mac and Linux only). GATK, Exomiser, bamtools, bedtools, cutadapt, bioawk, bioconductor, samtools, STAR, LUMPY, Qiime2, edgeR, DESeq2, HOMER, MACS2, Sailfish, kallisto, keras, BLAST, TopHat, StringTie and many more. For full list of applications please visit biogrids.org. Please note that all BioGirds applications are also available on HMS O2 cluster.

 

Biostatistics Services:

Biostatistics support is offered through a separate Biostatistics and Research Design Center, which is directed by Edie Weller PhD.  The Center includes PhD and Masters-level staff with expertise in quantitative and qualitative research methods.  Expertise in: pre-clinical experiments, clinical trials, observational studies (retrospective and prospective), longitudinal studies, randomized studies, health economics and econometrics, survey research, qualitative research, and high dimensional functional neuroimaging research. 

 

Biostatistics, Data Analysis and Visualization Software available to Pediatric Scholars:

For more information and immediate installation instructions please visit Pediatric Scholar portal

  • RStudio: An open source software environment for statistical computing and graphics is available for Macs through the BioGrids installer. There are many tools for the analysis and comprehension of high-throughput genomic data provided by Bioconductor (also available through the BioGrids installer).

  • SPSS Statistical Package, an easy to use general purpose statistical analysis program is offer free-of-charge to all members of the BCH community and educational sessions for SPSS are offered through the BCH Bioinformatics Core..

  • MATLAB: a standalone version of Matlab for Macs and PC is available. BCH also licensed the following toolkits.

  • Through Pediatric Scholar we also offer access to PASS, SAS, StataGraphPad Prism, Mplus, and Nvivo. Additional statistics software: Mathematica and JMP are available through HMS Countway Library.

 

Structural Biology Services:

 

Support for structural biology laboratories at BCH is offered through SBGrid. For more information please schedule an appointment with Dr. Sliz, by writing to research.computing@childrens.harvard.edu.

Relevant Web  and Intranet/Restricted Links: SBGrid, Cryo-EM at Harvard.

Support areas include:

  • Software: over 400 software titles are managed by SBGrid Consortium and can be installed on Mac and Linux computers in your lab. Please visit the SBGrid Software portal for the full listing.

  • Infrastructure: SBGrid Advanced Computing Team (ARC) supports structural biology workstations

  • Data: SBGrid Data Bank provides a portal for deposition of experimental datasets.


Infrastructure and High-Performance Computing Services:

 

Several HPC and specialized hosting resources are supported by the RC services team, which is lead by Jurvis LaSalle. To schedule an informational appointment with Jurvis to discuss hosting services, to inquire about our partially-subsidized HPC services, or to obtain more information about current projects please contact the RC Help Desk via email at research.computing@childrens.harvard.edu

 

Most frequently utilized resources include:

 

  • Amazon Web Services: BCH researchers may utilize AWS computing resources, which with further approval, can be also used for computations with patient level data. Users will need to provide a fund number to offset compute costs, or can utilize NIH Commons Credits (to apply for credits please visit the NIH Commons Pilot Website).

  • Virtual Server Hosting: Host an inexpensive server at Children's. Processing is handled by a few very powerful servers; the benefits include lower cost, lower power consumption and high reliability. Research Computing hosts over 600 virtual servers. $125/quarter and up.

  • Physical Server Hosting: Researchers whose computational needs exceed those provided by our virtual servers can purchase their own equipment and co-locate it in our Needham Data Center (NDC) for $112.50/rack unit/year. NDC is a lights out facility that has no regular staff. Servers placed here should be designed to be highly available or with the understanding that it may be several days before someone can physically touch the system. There is a $100/hr escort fee should RC staff have to chaperone an external vendor’s visit to NDC.  

  • Lab Hosted Server Support: With an enrollment into RDS, the RC HPC team will support hardware/OS issues and provide guidance for configuring network and mail relay. Custom application support/server services would not be provided.

  • Services Hosted for other BCH departments: the RC HPC team consults with you for your custom computing needs. We have helped a number of groups deploy custom solutions to achieve their goals (CHeRP, Granite, CarraNet, REDCAP, InForm, BioBank, CareWare, OpenShift, etc).

  • Web Hosting: labs with simple web site needs can deploy a static HTML website on our existing web server. Labs with more complex web site needs should request a dedicated virtual server.

  • Database Hosting: Research computing provides encrypted MySQL database hosting. ISD has Oracle and MS SQL database clusters available for your use.

  • Pediatric Scholars have access to a small BCH HPC cluster (80 Intel Xeon CPU E5-2698 v4 @ 2.20GHz cores, 2 Tesla K80 cards, Slurm job schedulers).  BioGrids collection of biomedical applications is already installed and ready to use.

  • We can also facilitate access to O2 (formerly Orchestra, 8062 cores) cluster at Harvard Medical School. Although this resource is servicing primarily the on-quad faculty, BCH faculty with primary appointments at HMS and affiliated faculty can also utilize this resource. Biogrids software stack is preinstalled, and job scheduling is handled by Slurm.

  • Google Cloud Platform (GCP): Access to BCH instance of GCP is currently limited to BCH researchers with NIH Commons accounts and to strategic projects. No PHI can be stored on GCP.

  • XSEDE National Cyberinfrastructure: XSEDE is an NSF-funded virtual organization that integrates and coordinates the sharing of advanced digital services, including supercomputers and high-end visualization and data analysis resources. To apply for time on XSEDE please visit Startup Allocations. Research Computing can work with individuals to prepare technical project description and provide more information about XSEDE resources.

 

Retrospective Studies

 

The Clinical Research Information Technology (CRIT) team, which is lead by Mohamad Daniar can help you through the entire cycle of the clinical trials process (in collaboration with others, as noted below). 

 

Supported areas of discovery include:

 

  • BCH Electronic Health Records: queries of our research data warehouse should be performed through a modern TriNeX interface, and can be subsequently expanded in our i2b2 instance (all 1.8M BCH records). In collaboration with Biobank we also maintain an i2b2/tranSMART instance to support Biobank queries (5,000 records).

  • BCH Whole Genome and Whole Exome Sequences: Queries of our genomic data warehouse should be performed through the state-of-the-art WuXi NextCODE interface. The genomic warehouse is managed by RC Bioinformatics and Genomics team.

  • BCH Clinical Notes: Hound Dog system can be used to search BCH collection of 1.7M clinical notes.

  • Global Electronic Health Records:

    • Accessible Research Commons for Health (ARCH), with BCH PI Dr Marc Natter, offers access to data from Boston Children’s Hospital, Beth Israel Deaconess Medical Center, Boston Medical Center, Partners Healthcare, Grady Memorial Hospital, Morehouse School of Medicine, University of Texas Health Science Center at Houston, BJC Healthcare, Wake Forest Baptist Health and additional Tier II sites.

    • Starting in September 2019 we will offer access to Cerner Health Facts database,  with over 150 million patients and 1.3 billion laboratory results, collected from 100 US institutions. The database includes data on patient demographics, encounters, diagnoses, prescriptions, procedures, laboratory test, locations of services/patients, hospital information, and billing.

 

Prospective Cohort Studies

 

CRIT team can help you through the entire cycle of clinical trials process (in collaboration with RC Application Services and Infrastructure Services teams). 

 

We are one of the cores of Institutional Centers for Clinical and Translational Research (ICCTR), and our areas of support span:

 

  • Preparatory to Research Activities: BCH cohort discovery queries should be performed through a modern TriNetX interface, and can be subsequently expanded in i2b2 instance. We also offer access to a state-of-the-art whole genome query system with WuXi NextCODE.

  • Industry Trials Match: De-identified BCH patient population is advertised to industry on the TriNetX network. BCH investigators are notified when a patient has an enrollment opportunity.

  • Protocols Management: CHeRP system, which is used to submit and maintain research protocols, is being developed by Research Administration (Frank Thyer’s group) and is maintained by RC.

  • Regulatory Binders Management: BCH currently pilots Complion electronic regulatory binders system (dozen of trials in Pulmonary and Genetics). At the conclusion of the pilot we will consider expansion to other divisions.

  • Consenting Process: In collaboration with Beth Israel Deaconess Medical Center, with support from Catalyst we have recently developed a Paperless Consenting REDCap system for eConsenting and remote consenting. Please contact Ram at RC Help Desk for more information.

  • Electronic Data Capture (EDC): RC  currently operates four EDC systems:

    • BCH REDCap to capture survey data (including PHI) and create databases with access limited to BCH network

    • Open REDCap for collaborative projects

    • Inform for Part 11 compliant data capture

    • Pilot instance of REDCap Cloud to support Part 11 compliant capture of research data and patient-reported outcomes

  • Mobile EDC

  • Custom Data Requests: Researchers with approved study protocols can request identified patient-level data through CRIT data request process (access to Electronic Health Records and Clinical Notes).

  • Special Data Request: In collaboration with IRB, Compliance and Office of General Counsel, we also review request for data request and computational process which fall outside of BCH routine framework.

 

Coding Shop Services

Biobank Informatics team, lead by Ram can assist you with various software development project. To schedule an informational appointment with Ram to discuss coding services, to inquire about our partially-subsidized RC services, or to obtain more information about current projects please contact the RC Help Desk via email at research.computing@childrens.harvard.edu

 

The research computing Coding Shop works directly with researchers to develop custom research applications, reports, and dashboards. With expertise throughout the development lifecycle, engineers in the coding shop use agile project management from the requirements gathering stage through to testing and deployment.

 

Digital Science Education

 

Research Computing connects researchers with internally and externally developed training opportunities. We offer nanocourses, trainings, info sessions, office hours, NetLearning modules and articles on Genomic Analysis, REDCap, TriNetX, DropBox and more. Please check out our calendar that lists trainings offered by Research Computing, the BCH Medical Library, the Countway Library and HMS Research Computing that are available to any BCH researcher. We have knowledge base articles available in Google Team Drives  and through JitBit. We also have several NetLearning modules available and offer online seminars and trainings via our YouTube channel: BCH Digital Science TV.

 

 Relevant Web  and Intranet/Restricted Links: Nanocourses, Calendar, Office Hours, NetLearning, and BCH Digital Science TV. 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

PEOPLE

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Piotr developed a global computing infrastructure for structural biology (sbgrid.org) and has been coordinating research computing at BCH since 2016. He is a structural biologist and can advise you on many aspects of bioinformatics and computational biology.

CRIO

Associate Professor

PIOTR SLIZ, PhD

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Jurvis is leading the BCH High-Performance Computing team and coordinates access to advanced resources, including computing clusters, virtual machines, cloud resources and collaborative compute infrastructures. 

HPC Manager

JURVIS LASALLE

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Josh coordinates desktop support for ~1700 subscribers of Pediatric Scholar and RDS services. His group handles ~200 requests per week. They have seen it all!

Desktop Support Lead

JOSH LOPEZ

Medical Record Analysis

Outsource your coding projects to Ram and his team! They have recently released BCH electronic and remote consenting software and developed a Microstrategy portal for Biobank. 

Coding Shop and Biobank Lead

RAM CHAKRABARTY

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Shira coordinates BCH Connect Genomic Data Commons, is an expert in WuXi NextCODE software and has recently taught a popular course on genomics. She is also coordinating bioinformatics consulting support at BCH and will advocate for your projects. 

Bioinformatics & Genomics Lead

SHIRA ROCKOWITZ, PhD

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Kris can help you craft data management policies for federal projects and advise you how to use DropBox and G Drives to protect your data. Ask her how to publish data with Dataverse!

Data Management Consultant

KRIS BOLT

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Mohamad coordinates CRIT support and infrastructure, including REDCap, Inform, Data requests, and Clinical Data Research Networks services.

Clinical Informatics (CRIT) Lead

MOHAMAD DANIAR

Pharmacist  in aisle of Pharmacy

Jen is coordinating coding of Part 11 compliant EDC with Inform and REDCap Cloud. She also specializes in TrinetX interface and teaches many RC courses.

CRT Team:

TrinetX Product Specialist

Inform Product Specialist

JEN WARTICK

Listening to baby's lungs

Jim is managing the clinical notes search application and can assist users with queries.

CRT Team:

Hounddog Product Specialist

Inform Product Specialist

JIM GREGORIC

CONTACT RC Help Desk

Please note, that in general, all clinical systems at BCH and centrally managed workstations are supported through the ISD Help Desk. The ISD Help Desk can also assist with password resets and network connectivity. You can contact them 24/day via the methods listed here.

 

Research Computing (RC) Help Desk provides more specialized support for individually managed research computers (desktops and laptops) through Pediatric Scholar service.  In addition, RC Help Desk coordinates support for a wide range of scientific services, including Genomics, Bioinformatics, Retrospective Studies, Clinical Trials, Discovery, Electronic Data Capture, High-Performance Computing, Data Management, and Compliance with Research Computing Policies.