FAQ

A: If you search for a standard topic recognized by NextBio (e.g. a gene or a disease name) the default page that comes up is that topic's home page with correlated data results. If you want to search for everything that matches your keyword you can select the "See other results" link. It will take you to various items with titles, descriptions or synonyms matching your keyword search. top

A: 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 will show up ranked at the top. NextBio's algorithms also include additional normalization for gene ranks based on platform size and other factors. top

A: 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 correlation p-value), this will rank that experiment at the top when the search with Biogroup X is performed. top

A: 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 search results 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. top

A: NextBio indexes over 17 million abstracts from the public domain. 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 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

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A: 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 a lot of non-specific text. top

A: We provide all of our users the ability to upload, save and manage data and place it within the context of world's experiments. You can import an unlimited amount of data for free if you choose to share it with the rest of the community. If you choose to keep your data private beyond the initial trial period, you will need to subscribe to NextBio's premium account. top

A: Free users can upload an unlimited amount of data for free if they do not restrict access to that data. If access is restricted through user-controlled privacy settings, a subscription fee will be charged. top

A: 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 contain 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. Accetable formats include text, csv and Excel. We currently do not support Excel 2007 formatted files, but plan to do so in the near future. top

A: You can upload report, presentation and other files associated with a given study. They don't need to be in any particular format but are limited to 5MB. These files are not required to complete data import - they can also be added at a later time. top

A: 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

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A: 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. top

A: You can upload your bioset files into a new study or existing study (only if the biosets are from the same organism as the target study). top

A: 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. top

A: 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). top

A: 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. top

A: You can use the Library to browse public studies or organize, edit and browse your organization's internal data (enterprise users). top

A: You can search for information on a gene of interest, pathways and other functional sets, tissues, diseases and compounds, among other things. You can place all of your searches within the context of the world's experimental data (based on relevance), as well as all available literature. top

A: 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. top

A: Select the study in the Library Explorer navigator (on the left). The Study Inspector (on the right) will contain a panel that allows you to edit your tags. top

A: 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. There is no free search for our enterprise product; each user needs to be authenticated before accessing it. An admin can control which users get on 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. For more information, please refer to our enterprise solutions section. top

A: 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. top

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

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

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

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

A: 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. top