General Questions

What is NextBio?

NextBio is the provider of an innovative platform that enables life science researchers to search, discover, and share knowledge locked within public and proprietary data. NextBio's platform seamlessly combines powerful tools with unique correlated content to transform information into knowledge, providing the foundation for new scientific discoveries. With NextBio, in just one click you can search tens of thousands of studies containing billions of data points spanning different experimental platforms, organisms and data types. NextBio helps organizations increase productivity and dramatically improve collaboration across therapeutic groups and geographic boundaries. NextBio is delivered as a SaaS (Software as a Service) solution resulting in quick deployment and rapid return on investment.

Who should use NextBio?

NextBio is designed for use by anyone interested in basic and clinical research, drug discovery, or biology. Through NextBio you can discover the functions of your gene of interest, understand its role in disease, and identify novel biomarkers. You can also discover novel associations between diseases, treatments and tissues, or compare your own data with the world's experimental results. NextBio's literature search will enable you to quickly relate any interesting findings to published articles. Finally, you can also collaborate and network with other researchers within and outside your field using NextBio.

What can I search for?

Using NextBio, you can search for genes, pathways, diseases, tissues, compounds, authors, phrases or any other item of interest. When you search a biological entity that matches a term in auto-complete, you will be presented with a list of categories of related results, including Data Correlations, Literature, Clinical Trials, and News. The Data Correlations result page will include meta-analyses or high-level ranked summaries of results across categories (i.e. associated diseases in the case of a gene search). Search is not limited to single terms. You can also search using phrases or include Boolean logic (OR, AND, NOT) with terms. Finally, Professional and Enterprise users can begin a query by starting with an imported dataset or a public dataset to find highly-correlated datasets and biogroups.

Where does NextBio's public data come from?

NextBio's content includes pre-processed data from public resources such as NCBI GEO (Gene Expression Omnibus), ArrayExpress, SMD (Stanford Microarray Database), and many others and then processes the data to narrow down to statistically significant findings. Users and organizations can also bring in their data and keep it private or share it with a select group of individuals (via NextBio Professional or NextBio Enterprise Editions).

What types of data does NextBio currently support?

NextBio currently supports any type of gene-centric data (gene expression, proteomics, microRNA expression, etc.) for human, monkey, mouse, rat, fly, worm, and yeast. NextBio Professional and Enterprise Edition users can also import many sequence-centric data types and correlate the results with other datasets (gene- and sequence-centric data). Sequence-centric data types supported by NextBio include comparative genome hybridization (CGH), genome wide association studies (GWAS), chromatin-immunoprecipitation (ChIP) on-chip studies, ChIP-seq studies, RNA-seq studies and more.

Does NextBio plan to expand support for other data types?

At NextBio we continue to incorporate new data types into our search platform and enhance data in many ways. To this end, we are looking at new data types, new platforms for supported data types and new species to support.

What are biosets, biogroups, and studies?

See the terminology page for definitions of these and other terms.

What NextBio features are free?

Searching all publicly available data and literature in NextBio is free. Moreover, with free registration, you can save study results (data and literature) as bookmarks and forward them to colleagues. You can also create a user profile, where you can organize your research projects and list your publications. NextBio also provides subscription-based versions of its products, NextBio Professional and NextBio Enterprise. NextBio Professional allows data import and correlation of the imported data against all public data, advanced search and query features, and technical support. NextBio Enterprise features unlimited data import, special APIs for bulk import of data, advanced search and query features, an administration dashboard for user access control and settings, and technical support.

What are the benefits of upgrading from NextBio Basic to NextBio Professional?

NextBio Professional allows individuals or companies to securely upload internally-generated experimental datasets and compare them directly with public data. NextBio Professional also includes hundreds of additional sequence-centric studies (CGH, GWAS, ChIP-on-chip, ChIP-seq, RNA-seq, etc) to examine and prepare to. A single researcher or group of researchers can effectively exploit these results to validate existing results, while formulating more informed hypotheses.

What are the benefits of upgrading to NextBio Enterprise?

NextBio Enterprise provides pharmaceutical and biotechnology companies, commercial and non-profit R&D organizations, and academic institutions with a completely integrated solution that enables a dramatic increase in research productivity andbetter leverage of investment in past and ongoing experiments. NextBio Enterprise integrates data in disparate formats from isolated silos to a common platform, allowing. researchers across organizations to leverage others' findings tobetter inform their own research efforts. With NextBio Enterprise, companies can upload unlimited amounts of internally generated experimental data and correlate it against itself as well as against all public data.

How can I schedule a demo of NextBio Professional or NextBio Enterprise?

You can request a personal demo of NextBio Professional or NextBio Enterprise by sending an email to demo@nextbio.com, or calling (408) 861 3610.

How were the terms that are available through auto-complete and shown in tag clouds selected?

Terms were extracted using the following ontologies and indexes:

Genes: NCBI Gene Indexes

Diseases: SNOMED CT®

Tissues: MeSH (Medical Subject Headings from National Library of Medicine)

Compounds: Curated compilation of MeSH & PubChem (NCBI)

Biogroups: GO (Gene Ontology Consortium), MSigDB Pathways (Broad Institute), and InterPro Protein Families (EMBL-EBI)

Organisms: MeSH

SNPs: dbSNP (NCBI)

Authors: Medline

Search-Related Questions

What does the Data Correlations page show?

The Data Correlations results page lists all studies (including your private studies) which correlate with your search term(s). A meta-analysis of all significant results helps to identify top matches across related categories. For instance, by searching with the SOX9 gene, you can find over 1200 studies in which significant results for this gene are found. If you're interest is in cancer, you can refer to the meta-analysis over disease, and click on ‘melanoma', a top-matching hit, to view the focused subset of studies that contribute to this finding. Once you select a group of studies based on a meta-analysis category, you can drill down to see the supporting statistical results for the gene from each study.

How does the Filters section of the Data Correlations page work?

The 'Filters Applied' section on the Data Correlations page allows users to narrow down individual study results by any combination of species, data type(s), and keywords. For instance, you can search through all 1700+ studies with which the gene, IGF1, is associated, or you can filter your results to include only the human and monkey RNA expression experiments tagged with brain, for a more focused and manageable result.

What does the Studies & Projects page display?

The Studies & Projects section allows you to access studies according to your permissions. In other words, you can view just your studies, just those studies you have access through specific projects, just public studies or all studies.

What is the purpose of the Literature page?

The Literature page shows the results of a literature search; in other words, view a list of publications which match your search term, listed in order of relevance. You can click the "Date" link above the results to sort the list of articles by publication date instead. In addition, NextBio extracts key biomedical terms dynamically from the results (abstract and full text when available) and displays them via a tag cloud. You can use any term in the tag cloud to further filter and refine your search results.

What does the Clinical Trials page display?

The Clinical Trials page lists all individual clinical trials relevant to your search term. Clinical trials are listed in order of relevance but can be reordered by ‘last update date' via the "Date" link. As with literature, you can further refine your results using any of the terms that appear in the associated tag cloud.

What does the News page display?

The News page lists individual news results relating to your search term from hundreds of available biological and health-related news sources. As with the Literature and Clinical Trials pages, news articles are listed by relevance, but you can click the 'Date' link to see the list ordered by date. Additionally, a tag cloud of co-occurring terms allows additional filtering possibilities.

For a gene search, what does the corresponding link to the Gene Details show?

The Gene Details section provides a summary of gene information. Here you can find information such as alternate names, links to gene orthologs, known transcription factor and miRNA binding sites for the gene, and membership in existing gene ontology lists, pathways and protein families. Additionally, NextBio Professional and Enterprise users can launch the NextBio Genome Browser from this page to view a graphic representation of the gene in chromosomal context.

How does the "auto-complete" function work?

The auto-complete function simplifies the selection of genes, pathways, tissues, authors, SNPs, and other biomedical concepts by providing a drop-down list of matches for you to pick from as you type. In order to provide the most appropriate suggestions, it uses a combination of biological and medical ontologies and other proprietary heuristics. The use of "auto-complete" is optional, and you can simply type in your term and press the Enter key to bypass it.

How does NextBio rank Data Correlation results when I search for my gene of interest?

NextBio ranks all of the studies for a given gene based on the activity of that gene in each individual experiment. For example, if a drug induces the activity of "Gene A" more than any other gene in a dataset ( or "bioset"), Gene A will get the highest rank amongst all genes profiled in that individual study. If you query Gene A in NextBio, the bioset mentioned above, which gives Gene A a ranking of 1, will show up ranked higher than another bioset where, for instance, it is the 5th highest-induced gene and given rank 5. NextBio's algorithms normalize gene ranks based on platform size and other factors.

How does NextBio rank Data Correlation results for a biogroup of interest?

Biogroups represent any set of genes or proteins that share some biological property, such as function or common regulatory motif. NextBio uses proprietary rank-based statistics to correlate biogroups with experimental data. If the majority of genes encoding proteins involved in the MAPK signaling pathwy are highly active in a given bioset (resulting in a corresponding low (or significant) p-value, this bioset will be highly ranked in the results of a NextBio search of MAPK signaling pathway.

How does the NextBio rank results for my tissue, disease or compound of interest?

NextBio uses a combination of its proprietary rank-based statistics and various meta-analysis techniques to compute the most significant genes and biogroups associated with a tissue, disease, or a compound under investigation. To perform this calculation, NextBio combines all studies related to a given topic to identify the most significant genes and functional trends. This enables you to glean information from the standpoint of "collective experimental intelligence". On the top of the Data Correlations results page, you can see a list of the best-correlated genes and biogroups for your search term, and a list of all the relevant studies below. When you select a ranked gene or a biogroup of interest, you can then access a subset of studies related to your original term but limited to those matching the selected gene or biogroup.

How does filtering of results work?

On the Data Correlations search page you can use filters to narrow down a large list of matching results to a restricted subset according to organism, data type or keyword. Within text-based search results (Literature, Clinical Trials and News), enter any term in the filter box to narrow results.

What criteria does NextBio use to rank relevant literature matches for a search?

NextBio indexes over 19 million abstracts from PubMed and over 130,000 full-text publications from PubMed Central. For its literature search, NextBio uses a number of heuristics, including:

• Extensive ontology with relationships between terms, synonyms, as well as a term hierarchy
• A customized domain-specific stop word list and analyzer that emphasizes ontology terms
• The authority of the journal where the paper was published
• Date of publication

Tag Cloud Questions

What is a tag cloud?

A tag cloud shows a list of relevant terms (tags) extracted from the text results of your search. These are terms that co-occur in the abstracts and text of articles in which your search term has been found in. Tags are arranged alphabetically within the tag cloud; the bigger the font the more strongly associated the tag is to your search term.

How can we obtain more information from a tag cloud?

The number of documents analyzed increases as you go from 50 (default) to 200 to 1,000 results (i.e. abstracts) analyzed. The amount of time taken for computing also increases with each level. Select to analyze the top 1000 abstracts for an even more informative tag cloud. Additionally, switch to sub-categories of terms (such as authors) to expand on selective types of information.

Community and My NextBio

Why should I create a personal user profile on NextBio?

A personal profile page on NextBio is an online scientific CV, where you can list positions, degrees, and publications. Your NextBio profile is linked to our comprehensive literature search, so you can easily claim your journal articles as your own. With a personal profile you can save search results and organize them by project. You can also join the NextBio community once you create a personal profile.

Can I control who sees my profile?

Users have complete privacy control over their own profiles. NextBio makes it easy for your profile to be seen by only your groups and contacts, only registered members of NextBio, or all users of NextBio. Read our privacy policy.

What is the Recommendations feature?

The Recommendations feature allows you to receive studies, literature, clinical trials, and news based on your recent searches and research interests.

What is the NextBio Community?

The NextBio community is made up of users and groups in the NextBio system. Our users come from a broad range of organizations, including research universities, as well as biotechnology and pharmaceutical companies all over the world.

What are NextBio contacts?

NextBio Contacts are your personal online scientific community - colleagues, lab mates, and collaborators. These can be people from your own lab or institution as well as NextBio users with similar research interests or backgrounds.

Who can I add as a NextBio contact?

Any registered user can be added as a NextBio contact. People who are not yet members of the NextBio community can also be easily invited to join as a contact.

Who can I search for under "People"?

You can search for all registered users of NextBio that have allowed their profiles to be searchable. Please see our privacy page to set your personal privacy settings. If you do not see a colleague listed on NextBio, it is still easy to invite them to join the NextBio community.

Why create groups?

Groups are an easy way to collaborate and communicate with a small group of people you work with or a large number of users with research interests similar to your own. Currently, you can share studies and participate in discussions with other members of the groups. In the future, NextBio will add the ability to share publications, bookmarks, and other types of information with group members.

Can I control who can join a group?

As the creator or administrator of a group, you have full control over group privacy and membership. Groups can be public, allowing all members of the NextBio community able to join, or can be private requiring invitation by the administrator. Groups can also be invisible to the public, so that they do not appear in search results.

Can I share my data with other group members?

NextBio Professional or NextBio Enterprise users can easily upload their own data, compare it with all public data in the NextBio system, as well as share it with group members. We value your privacy and data security at NextBio. You have complete control over who sees your own data.

What happens when I archive a message?

Archiving messages removes messages from your inbox without deleting them. In the inbox, click on "archived inbox" in the drop down to see all archived messages.

Data Import Questions

Data import functionality is available to NextBio Professional and NextBio Enterprise users.

Can I import my own data privately?

As a NextBio Professional and NextBio Enterprise user, you can upload, save, and correlate your own data with public data.

What is the acceptable data format?

You can easily upload data files to the NextBio platform as processed raw data - results of statistical analysis consisting of genes/proteins or custom IDs and associated statistics (in text, csv or excel file formats). NextBio enables users to import standard statistical columns fields (fold change, p-value, score, rank, correlation) and custom columns with numbers and any user-defined titles (a maximum of 5 columns). The Gene identifier column should be in the left-most column or should have the header "Gene name" to be recognized (see example below). The minimum requirement for upload of your data is that your file contains a list of recognizable identifiers (e.g., a set of genes). For experimental data, we strongly recommend including associated statistics in order to improve the quality of the correlation with other data within NextBio. You can import individual files by adding them one by one, or you can zip them into a single file for easier upload. Acceptable formats include text, .csv and Excel (including both .xls and .xlsx files).

What should I upload as associated files?

You can upload report, presentation and any other files associated with a given study. They don't need to be in any particular format but are limited to 1MB. These files are not required to complete data import and they can be added at any time.

How does NextBio rank features in my dataset during import?

NextBio uses standard fields described above to rank features in your gene/protein set. If more than one standard statistical column is present, NextBio automatically picks one of the following columns (in order) for ranking:

• Fold change
• P-value
• Score
• Rank
• Correlation

What type of gene and protein identifiers does NextBio support?

NextBio recognizes most public and standard commercial platform identifiers, including NCBI Gene IDs, Gene symbols, NCBI accession numbers, ENSEMBL IDs, RefSeq identifiers, IPI ids, and custom IDs from most Affymetrix, Illumina, Agilent and GE Healthcare platforms.

Can I upload more biosets into an existing study?

Yes, you can upload bioset files into a new study or an existing study, provided the biosets are from the same organism and data type as the target study.

Why should I tag my data?

Tagging is an important process which provides semantic structure to your data. While it takes just a few seconds to tag data, the benefits are significant. Search results are significantly improved once the data is tagged. Furthermore, tagging can be used to associate your study within an appropriate context and can help contribute to additional computations (Enterprise users). Tagging also helps your colleagues and collaborators quickly understand the biological background of the study.

What criteria should I use to tag my data?

You should tag each of your datasets with the following: 1) the tissue or cell line under study, 2) the disease, if applicable, and 3) genetic or chemical modifications (compound or a gene, if applicable). In general, tagging should only describe the main attributes of the experimental design and not of the experimental result or observation (e.g., you shouldn't tag your data with a highly expressed gene you detected in your microarray results).

How does NextBio correlate my data with other data?

NextBio uses proprietary rank-based statistics to compute associations between the data you import and all other experimental data. This allows you to place your experimental results within the context of the world's experiments in order to validate your study results, discover novel associations and trends, and design new experiments. NextBio correlates your data with all biogroups as well, allowing you to discover common features among the genes or proteins that comprise your study. This, in turn, provides a greater understanding of the cellular events contributing to your study's results.

How do I edit studies that I have already imported?

To edit an existing study, click on the "Studies & Projects" link in the left vertical panel of the NextBio homepage. Select the "My Studies" tab, and click on the "Full Study Details" button corresponding to the study of interest. The pencil icon or an "Add" link indicates sections where you can apply changes to "Study Details", "Bioset details", and "associated files". You can also delete any or all biosets within your individual studies.

How do I edit the tags for studies that I have already imported?

To edit tags for an existing study, click the "My Studies & Projects" link in the left vertical panel of the NextBio homepage. Select the "My Studies" tab, and click on the "Full Study Details" button corresponding to the study of interest. Click on "+Add Tags" or "Edit" in the tag section under the "Biosets" tab.

Advanced Query Questions

Advanced Query is available to NextBio Professional and NextBio Enterprise users.

What is Advanced Query?

Advanced Query enables users to query with a collection of individual biosets to derive a consensus gene signature and/or discover sets of commonly regulated biogroups. This allows you to identify the most consistently and highly regulated genes across multiple biosets. Biosets can be mixed and matched from both your private data library as well as the NextBio public library. The current advanced query allows users to search up to 50 biosets at a time.

How do I run an advanced query?

Find the Advanced Query box at the bottom of each Data Correlations page. Drill down to the "biosets" level of each study by clicking on a study title. Click on the icon found to the left of any bioset that can be added to the advanced query. Such biosets will typically be accessed during your review of individual studies. You may browse to other pages to find more biosets to add; the advanced query box will remember all biosets already added. Click on the "Open" button in the upper left corner of the advanced query box if you need to expand it. Click on the "Run Query" button to execute it.

How do I save the results from an advanced query?

From the results page, choose to "Export Results" to an excel file. Alternatively, you can save the results page as a bookmark for later access.

What can I put into Advanced Query?

You can add up to 50 biosets spanning different platforms, organisms, projects and libraries.

Can I change my advanced query after running it?

NextBio remembers your most recent advanced query until you sign out. You can continue to add or remove biosets and run the altered query. To start a new query, click the "remove all" link from the advanced query box.

How do you compute the most significant genes in the advanced query?

There are a number of parameters which are used for computing the most relevant genes. The most important two parameters are the activity level of a gene in each bioset and the specificity (the number of biosets in which the gene is active).

Enterprise-Related Questions

How can my organization use NextBio?

Through NextBio, your organization can leverage all of its internal large-scale data to benefit the entire R&D team. All imported data within an enterprise is cross-correlated to previously uploaded internal data and to the public data. NextBio provides a secure SaaS solution for enterprise customers. Each enterprise has a customized domain with configurable security controls in place to be compliant with your enterprise's security policies. All access to this domain is over HTTPS. Each user is authenticated before they can access their organization's version of the enterprise product. An administrator can control which users have access to the system. Data can be associated at the domain level and shared across all users in the domain. The results seen for the same query by users across different domains will vary and are a function of the data that each domain is authorized to access.

How do enterprise users access NextBio?

Each enterprise user needs to be registered for their enterprise domain. Each domain has a unique URL. You should contact your NextBio representative or send an email to nbadmin@nextbio.com to get the URL associated with your domain. NextBio also provides a single sign-on option that transparently logs an enterprise user in.

What is the Enterprise Single sign-on functionality?

The NextBio Single Sign-on (SSO) solution uses a simple scheme of auto-registration and authentication of users from a trusted source, using specific HTTP headers or URL parameters in end-user requests. Through the NextBio single sign-on process, an existing user is transparently logged into the NextBio application. For a new user, NextBio creates a new account in the background and logs in the user without asking for a password.

NextBio provides two solutions for integrating single sign-on (SSO) for an enterprise. The first solution is a proxy-based solution. In this solution, all user requests from the enterprise are directed to NextBio through a trusted proxy, which provides authentication credentials to NextBio for the user. The second solution is a portal-based solution. With this solution a user logs into an internal portal within the enterprise to access NextBio. The trusted portal passes authentication tokens for a user to NextBio.

Will my organization's data and user activity on NextBio Enterprise be secure?

NextBio provides a highly secure solution for its enterprise customers. Please refer to the section on security for more details.

How can my organization upload studies in bulk?

NextBio provides simple APIs to enable you to import studies in batch mode. Please refer to the integration section for more details.

Does NextBio provide APIs?

We make a number of APIs available to enable you to bring data into and out of NextBio. Please refer to the integration section for more details.

How can we control data sharing and collaboration among different groups?

NextBio provides a feature where each user can create a private group and collaborate and share data only with users within this group.

Can we keep some data private from other users within an organization?

Users can easily control who views and has access to their data, both within their own organization and outside, through privacy settings. You can share data selectively with other individuals by creating a custom group and giving access to only those users that you choose.