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Resources FAQ

General Questions

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 through tens of thousands of study results with billions of data points spanning across 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 is NextBio useful for?

NextBio is designed to be used by anyone interested in basic and clinical research, drug discovery or biology. Through NextBio you can understand the function of your genes of interest and their roles in disease, identify novel biomarkers, discover associations between diseases, treatments and tissues, or place your own data within the context of the world's experimental results. The literature search enables you to quickly place any interesting findings within the context of published articles. You can also collaborate with other researchers using NextBio.

Where does NextBio's public data come from?

NextBio content includes pre-processed data from the public resources such as NCBI GEO (Gene Expression Omnibus), ArrayExpress, SMD (Stanford Microarray Database), and many others. In addition, individual organizations and users contribute data to NextBio for the benefit of the entire scientific community. Users and organizations can also keep their data private and share it with a select group of individuals.

What types of data does NextBio currently support?

NextBio currently supports any type of gene-centric data (gene expression, proteomics, siRNA screens, etc.) for human, mouse, rat, fly, worm, and yeast. We are actively working on adding support for monkey, plants and many other organisms.

What data types will NextBio support in the future?

Our goal at NextBio is to continuously incorporate new data types into our search platform. Gene-centric data is a natural starting place, but we are working on integrating sequence-centric, phenotypic, and other data types.

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 as bookmarks and forward them to colleagues, create your own user profile, 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 companies to securely upload internally generated experimental data and correlate it with public data. An individual researcher or groups of researchers can effectively exploit this data to validate against existing results, and formulate 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 a completely integrated solution that enables a dramatic increase in research productivity, better leverage of investment in past experiments, and improved collaboration across therapeutic groups and geographic boundaries. By integrating data in disparate formats residing in isolated silos to a common platform, researchers across the organization can leverage others' findings to better inform their own research efforts. With NextBio Enterprise, companies can upload unlimited amount of internally generated public experimental data and correlate it together as well as with 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.

What ontologies were used to extract the entities?

Terms were extracted from the publications using the following ontologies:

Genes: NCBI Gene Indexes

Diseases: SNOMED CT

Tissues: MeSH

Compounds: Curated compilation of MeSH & PubChem

Biogroups: NCBI Gene Ontology, MSigDB Pathways, and InterPro Protein Families

Organisms: MeSH

SNPs: dbSNP

Search-related Questions

What does the Data Correlations page illustrate?

The Data Correlations page summarizes the results from the search for all publicly available and personal data. For example, in the case of a gene search, you can view the list of normal tissues, diseases, and treatments in which the gene is highly up-regulated or down-regulated. You can click on a specific section, for instance, Diseases, to see a more extensive ranked list of results.

What are the Organisms and Data Types sections of the Data Correlations page?

The Organisms and Data Types sections on the Data Correlations page show the breakdown of the experimental data in the individual study results by organism and by data type. Click on any source to filter the experiments corresponding to that source.

What does the Studies page display?

The Studies section encapsulates the studies that directly investigate the gene, disease, or any other biomedical concept you are searching for. For example, if you search with IGF1, a study investigating the effect of IGF1 treatment of MCF7 cells will appear under Studies. Studies in which IGF1 is found to be regulated as a consequence of some other treatment or a disease will be found under the Data Correlations tab.

What does the Literature page exhibit?

The Literature page shows a list of publications for the search term. The publications are listed by relevance. However, click the "by date" link to order the list of articles by publication date. Key entities are extracted dynamically from the results and presented to the user via a tag cloud. Any term in the tag cloud can be used to further filter and refine your search result.

What does the Clinical Trials page display?

The Clinical Trials page sums up the individual clinical trials specific to the search term. The clinical trials are listed by relevance but click the "by date" link to order the list of Clinical Trials by "last update" date. Similar to articles, you can further refine your results using the terms in the tag cloud.

What does the News page exhibit?

The News page lists the individual news results for a given search term. As with the Literature and Clinical Trials pages, the news is listed by relevance but you can click the "by date" link to see the list ordered by date. As with articles, you can further refine your results using the terms in the tag cloud.

How does the "auto-complete" function with search suggestions 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. 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.

What can I search for?

Through NextBio, you can search for genes, pathways, diseases, tissues, compounds, or any other item of interest. You can also search NextBio using your own imported data. When searching for a gene of interest, for example, you can search for more details about the gene, which tissues and disease states it is significantly expressed in, and which compound treatments affect its expression.

How does NextBio rank results 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, Gene A will get the highest rank amongst all genes profiled in that experiment. When you search with Gene A, the experiment mentioned above which gives this gene rank 1, will show up ranked higher than another study where, for instance, it is given rank 5. NextBio's algorithms also include additional normalization for gene ranks based on platform size and other factors.

How does NextBio rank results for my biogroup of interest?

Biogroups represent any set of genes or proteins with a related function (e.g., cell cycle, MAPK signaling pathway). NextBio uses proprietary rank-based statistics to correlate biogroups with experimental data. If the majority of genes in a Biogroup X are highly active in a given experiment (which results in a very low, that is, significant, correlation p-value), this will rank that experiment at the top when the search with Biogroup X is performed.

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

NextBio uses a combination of its proprietary rank-based statistics with various meta-analysis techniques to compute the most significant genes and biogroups associated with a tissue, disease or a compound under investigation. To do that, NextBio pulls together 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". When you first get to the Data Correlations page for any topic, you see the top genes and biogroups for that search at the top of the page, and all other relevant studies below. When you select a gene or a biogroup of interest, the studies for that topic become ranked according to the activity of that gene or biogroup.

How does filtering of results work?

The text that you type in the filter box is compared against study and bioset names, bioset tags, and bioset descriptions. Study descriptions are not used in filtering since they often contain non-specific text.

What criteria does NextBio use to search for relevant literature?

NextBio indexes over 18 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:

the use of our 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; and
the date of publication

Community and My NextBio

Why should I create my personal 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.
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 — research universities, and biotechnology and pharmaceutical companies all over the world.
What are NextBio contacts?: NextBio contacts are a user's 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 easy to invite them to 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 made public, with all members of the NextBio community able to join, or made private, by invitation only. Groups can also be made invisible so that they do not appear in search results.
Can I share my data with other group members?: When you upgrade to NextBio Professional or NextBio Enterprise, you will be able to easily upload your own data, compare it with all public data in the NextBio system, and 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 allows you to remove messages from your inbox without deleting them. In the inbox, click on the "archived messages" check box 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 it with public data.

What is the acceptable data format?

You can easily upload data files to NextBio representing 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 (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 is that your file contains a list of recognizable identifiers (e.g., a set of genes). For experimental data, we strongly recommend to include associated statistics in order to improve the quality of the correlation to 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 - they can also be added at a later 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 picks one of the columns for ranking in the following order:

Fold change
P-value
Score
Rank
Correlation

What type of gene and protein identifiers do you support?

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

Can I upload more biosets into existing study?

You can upload your bioset files into a new study or an existing study (only if the biosets are from the same organism 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. The search is significantly improved once the data is tagged. Furthermore, tagging can be used to bring up your study within an appropriate context, or for additional computations (enterprise users). It also helps your colleagues and collaborators quickly understand the biological background of the experiment.

What criteria should I use to tag my data?

Tagging mainly consists of the following: defining the tissue or cell line under study, defining the disease (if applicable), and defining genetic or chemical modification (compound or a gene, if applicable). In general, tagging should only describe the main attributes of the experimental design, not of the experimental result/observation (e.g., you don't want to tag your data with a top gene you found to be interesting). See the NextBio list of tags and tag types.

How does NextBio correlate my data?

NextBio uses proprietary rank-based statistics to compute associations between the data you import and all other experimental data. In that way, you can place your experimental results within the context of the world's experiments to validate your study, discover novel associations and trends, and design new experiments.

How do I edit studies that I have already imported?

To edit an existing study, just go to the "My NextBio" link and select "my studies". After selecting a study of interest you can click the Edit button. You can easily change your study description or tags and add or remove associated report files. You can also delete any or all biosets within a give study.

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

To edit an existing study, just go to the "My NextBio" link and select "Studies" from the left vertical panel. After selecting a study of interest you can click the Edit button. You can easily change your study description or tags and add or remove associated report files. You can also delete any or all biosets within a given study.

Advanced Query Questions

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

What is Advanced Query for?: Advanced Query enables users to query with a collection of biosets to derive a consensus gene signature or ranked set of regulated biogroups. As a result, you can 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 query allows users to query with 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. 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 icon to the upper right of the advanced query box to expand it and click on the "Submit" button to execute it.
How do I save the results from an advanced query?: From the results page, choose to "Download Gene Results" or "Download Biogroup 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 changed query. To start a new query, click the "Remove all Biosets" button from the advanced query box.
How do you compute the most significant genes in the advanced search?: 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 for the benefit of 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 our 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 admin 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 and 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.