GeneDirector Frequently Asked Questions

1. What is GeneDirector?
2. Why do I need GeneDirector?
3. What kind of information does GeneDirector store?
4. Is GeneDirector the same as other LIMS?
5. I already have a lot of microarray data generated. Does it make sense for me to start using GeneDirector now?
6. Even if I import all my microarray data into GeneDirector, I still have to analyze these data piece by piece. This is very time and labor consuming.
7. Can I have my technician import all the data into GeneDirector and I (being the principal investigator) do all the high-level data processing?
8. We have a bioinformatician / statistician in our facility. I would like him to conduct data analysis for my project. Is this possible?
9. Our microarray data management needs are very different from most other laboratories in this area. How can we still use GeneDirector for our custom needs?
10. Is it possible to share the data with our collaborators?
11. What microarray hardware does GeneDirector support?
12. What database does GeneDirector use?
13. How does GeneDirector control data security?
14. Is it possible to access GeneDirector data directly in Oracle?
15. Do I need a full-time Oracle DBA for GeneDirector?
16. What OS does GeneDirector run on?
17. Is GeneDirector MIAME compliant?
18. Does GeneDirector handle Affymetrix data?
19. Is it possible to import and export large amount of data in GeneDirector?
20. How do I track the relationship of data in GeneDirector?
21. Is there a way to check the RNA quality?


1. What is GeneDirector?

GeneDirector is a comprehensive microarray data management system. It stores data at every step of a microarray experiment, such as probes, plates, array designs, arrays, samples, hybridizations, images, quantifications, as well as experimental protocols, manufacturers, materials, and compounds. Its integrated modules enable users to create array designs, process images, and analyze data, all in the same software.

2. Why do I need GeneDirector?

Each microarray experiment generates lots of data, such as probes, plates, array designs, arrays, samples, hybridizations, images, quantifications, and protocols. The size of the microarray data grows fast making data management a daunting task. Storing everything in files and folders not only makes it difficult to locate a particular piece of data, but also loses relationships between data.

In GeneDirector, microarray data are stored down to the probe level in an Oracle relational database to maintain the relationship and integrity. Users follow the microarray workflow to enter the data establishing the relationships between data. For this reason, every piece of data can be easily tracked down in the database.

3. What kind of information does GeneDirector store?

GeneDirector tracks the entire microarray experiment workflow. It stores data in every step of a microarray experiment, such as probes, plates, array designs, arrays, samples, hybridizations, images, quantifications, as well as experimental protocols, manufacturers, materials, and compounds. In addition, every data object can easily be customized to include site-specific properties, enabling GeneDirector to cover virtually all information related to microarray data.

4. Is GeneDirector the same as other LIMS?

GeneDirector is a microarray information management system. It has lots of similarities to conventional laboratory information management system (LIMS), but also includes microarray special software modules for array designing (CloneTracker), image quantification (ImaGene), and data analysis (GeneSight). You can conduct the entire out-of-lab microarray workflow within GeneDirector starting from the array design all the way to the comprehensive knowledge discovery from your microarray experiments.

5. I already have a lot of microarray data generated. Does it make sense for me to start using GeneDirector now?

Absolutely. Using the batch importers, you can import all your legacy data into GeneDirector. These data may include scanned images; GenePix *.gpr quantification files; Affymetrix *.CEL and/or *.CHP data files. After setting up the batch import wizard, all your legacy data may be imported into GeneDirector with a single click.

6. Even if I import all my microarray data into GeneDirector, I still have to analyze these data piece by piece. This is very time and labor consuming.

It sure is, and GeneDirector takes care of this as well. The batch image processing module embedded within ImaGene can process a large number of images altogether without any human supervision. Similarly, the cleansed array module can batch transform (including Lowess normalization) a large number of quantified arrays. These batch modules increase throughput and decreases human labor costs as well as promotes standardization.

7. Can I have my technician import all the data into GeneDirector and I (being the principal investigator) do all the high-level data processing?

Definitely. After your technician has set up a project for you and imported all the relevant data, he/she can transfer the project to you using the ‘Transfer Project’ feature. Once you are the owner of the project, the technician will no longer have ownership over these data. This is enforced to maintain data security.

8. We have a bioinformatician / statistician in our facility. I would like him to conduct data analysis for my project. Is this possible?

In GeneDirector, you can assign permissions to other users either to access your entire project or any part of the project. The above can simply be accomplished by permitting your data analyst to access your quantified array data.

9. Our microarray data management needs are very different from most other laboratories in this area. How can we still use GeneDirector for our custom needs?

GeneDirector Administration component offers properties to be defined and extended for every object in the GeneDirector. Any table in the database can be extended and specific requirements can be enforced to customize it according to your specific needs. For instance, the “Sample table can be extended to include a field called Organism. This can be used to store the information associated with the type of sample being processed. The Administrator can indicate if this is to be a required field or not, thus enforcing a minimum data policy. Furthermore the Administrato can create this field as a multi-valued field allowing the end-user only the option of selecting from the available choices such as Human, Rat, Mouse, Fly, etc. The user has to select from one of the items listed.

10. Is it possible to share the data with our collaborators?

Absolutely. Since we use an Oracle database back-end, it provides for unmatched security and flexibility. With GeneDirector, you can create multiple groups and administrators. We give the Administrator the ability to let any one or group of people have access to some or any part of the data. A user can be a part of multiple groups with different accessibility permissions assigned.

11. What microarray hardware does GeneDirector support?

GeneDirector is fully compatible with multiple hardware platforms, such as, Agilent, Axon, PerkinElmer, Applied Precision, BioRobotics, and Genomic Solutions.

12. What database does GeneDirector use?

GeneDirector uses Oracle as its back-end database because of its proven performance and security.

13. How does GeneDirector control data security?

In addition to Oracle’s security, GeneDirector controls data security by assigning permission to groups. GeneDirector administrator and owner of the data always have full control to the data, while the members of a group get access to the data through the group permission.

14. Is it possible to access GeneDirector data directly in Oracle?

Yes. GeneDirector provides open access directly through Oracle. Not only all the data are accessible in Oracle, BioDiscovery also provides the GeneDirector schema and application programming interface (API) for customer to build new tools onto GeneDirector.

15. Do I need a full-time Oracle DBA for GeneDirector?

Having an Oracle DBA on staff is helpful for setting up GeneDirector. But once being set up, GeneDirector itself is a low maintenance system. It does not need much attention besides normal backup, which an IT technician with a little knowledge of Oracle should be able to handle.

16. What OS does GeneDirector run on?

GeneDirector runs on Microsoft Windows 2000 and XP, UNIX, Linux, and Mac OS.

17. Is GeneDirector MIAME compliant?

Yes. GeneDirector is fully MIAME compliant. Not only GeneDirector has the all the data objects for microarrays required by MIAME, the configurations of each data object are also MIAME compliant.

18. Does GeneDirector handle Affymetrix data?

Yes. GeneDirector manages both Affymetrix and spotted array data. Affymetrix CHP, CEL, DAT, and EXP files can be imported and the quantified data can be analyzed with GeneSight, the data analysis module in GeneDirector. Affymetrix chip library files (CDF files) can be imported to create the array designs. GeneDirector also seamlessly integrates with GCOS (GeneChip Operating System) to track information related to arrays, such as barcode, lot number, etc.

19. Is it possible to import and export large amount of data in GeneDirector?

Certainly. GeneDirector can batch import and export quantified data in Affymetrix, ImaGene, and GenePix formats. In addition, it can batch import probes, plates, and samples.

20. How do I track the relationship of data in GeneDirector?

GeneDirector stores microarray data in relational database, that is, the relationships of the data are kept once the data are imported. To view the relationships, user just selects any data object and uses the Relationship Viewer to visualize the relationship among array design, array, biomaterial, RNA, labeled RNA, hybridization, scanned array, and quantified array.

21. Is there a way to check the RNA quality?

Yes. GeneDirector integrates with Agilent Bioanalyzer. The Bioanalyzer trace files (.cld files) can be imported to link with RNA samples and can be easily visualized.