Imaging data sharing

Imaging technologies become every day more important in scientific world. Several times in this blog we have talked about the advances of microscopy, fluorescence detection and in general imaging. Now we would like to analyze some problems related to data sharing. In 2008, the Journal of Cell Biology started the JBC Data Viewer, an online repository for original images in life sciences. The novelty of this tool is the possibility to preserve and share some information about instruments used, acquisition settings, image size and resolution. All these information are important to critically evaluate the data published. Indeed, the JBC Data Viewer collects only images previously published in scientific literature. Of course, such as a tool is extremely useful also because JBC Data Viewer is free for charge and authors have access to original data for viewing, simple measurement and review. This system doesn’t allow the download of original data and sophisticated image analysis and querying tools are not included in this application.

What are the main problems associated to the generation of a common repository of images? Every new platform must solve the basic problem of accessing the data contained in PFFs. Many commercially available microscope formats store their data in common formats, such as TIFF, DF5 or other formats that most software tools can read. In contrast, there is not an agreement about the metadata files and often data produced from competing companies are not compatible between them. For this reason, the standardization is required by all scientific community. Standards for biological imaging must be supported and developed, and once they are valuable for scientific discovery and data sharing, the community must demand the support of these formats in the commercial platforms.The challenge for software manufacturers is to find out an universal format that makes possible a data sharing in real time. It should be important to share not only final and published data but also the original images in order to better understand what has been the process to produce and correct the images self. The repository must be public and free for charges as in the case of JBC Data Viewer and the action must be concerted between public institutions, funding bodies and manufacturers. The final goal is quite easy to understand: scientific data founded by public money of non profit charities must be publicly available. Thus, in conclusion we hope that this repository will be soon available in order to continue the scientific advances also in the imaging field.

Electronic Lab Notebook

An Electronic Lab Notebook (ELN) is a software program designed to substitute paper lab books. Scientists and technicians to note their experimental results, protocols, observations and so on use such tool. What is the advantage despite using paper notebooks, currently broadly diffused in research labs?
ELN has been studied, as an interface in which is possible to collect huge amount of data, derived from several instruments. It’s possible to manage chromatograms, spectra, calculations, and statistics by using only one software. To this purpose, ELN must to be flexible and have an out of the box configuration in order to be customized in respect to scientific exigencies of scientists. Several scientists can simultaneously use the same ELN and all lab members can add their data; thus, a broad vision of overall laboratory workflow is always updated. This point is really important for big groups, where more than ten people work together and data sharing is not so easy for different reasons, such as failure of communications or lack of time. ELN may help scientists at this point, allowing better communications between them and facilitating data traceability inside the laboratory.

An immediate advantage of this global vision ensured by ELN is the perfect planning and managing of experiments: what has been already done is always updated and what still to be done may be recorded, saving money and time. ELN allows scientists sharing experimental information and raw data, even if they work in different places around the world. Real time data sharing is fundamental to collaborate in a productive and efficient manner. Of course, in this context security is a must. ELN has been set up in order to satisfy all requirements to prevent unauthorized changes without substantial collusion of otherwise independent personnel. Furthermore, giving their use in pharmaceutical industry ELN is expected to comply FDA regulation about software validation.
In particular, FDA is concerned with system integrity and falsification avoidance to guarantee correctness of scientific and pharmaceutical production. Good laboratory procedures and Good manufacturing procedure may require ELN to store and classify data, making ELN a fundamental tool also in quality control assurance. Indeed, ELN may be directly connected to instruments, such as pHmeter, refrigerator or balances and record calibration data. In this way, validation sheets are directly filled without further work of scientists.
Last but not least, ELN allows saving space, because it is paperless. Traditional lab notebooks and files folders need a lot of space to be stored, while it is really easier to back up an IT notebook. What are some of the best ELNs on the market today? Check out Sciency ELN at www.ruro.com/sciency. In conclusion, ELN will be an essential tool in all labs within few years and global science will be a reality!

Brain training is useless!

Commercially available brain trainings are computerized tests, developed and marketed with the aim to improve cognitive functions in children and adults. Basically, the use of this software may improve memory, problem solving, measure of reasoning and verbal short-term memory. Anyway, it has been noticed that in pre-school children video game players outperform not players in visual memory, but don’t have any other advantage in terms of cognitive improvement. To deepen this aspect, a large scale study has been carried out enrolling thousand of persons. Three study groups have been randomly assigned and each group has been trained on a specific task: the first one has been trained in planning and problem solving ability, the second one has been trained in a broader range of cognitive activities, from visual memory to attention, ad so on, the third group has to solve some general question by using every available source. This training lasts six weeks. At the end of the study statistical analyses reveal that each group have improved only in the specific task in which has been trained, but none general improvement of cognitive process in other task has been noticed. In conclusion, brain training tests don’t contribute to develop human mind.

IT system protection

The broad diffusion of technologies such as computers, databases, mobile phones and so on, has determined a considerable change in our life. We usually use this kind of instruments at the work or school, at home and in other situations of everyday life.
It’s really important that the global IT system would be safe and protected from hacking attacks. Last year, an important mobile phone manufacturer company found vulnerability in its system and phone calls could be listen by everyone knew this failure. This first episode started an intensive research on security system in order to preserve IT and our privacy. Scientists were called to identify flaws into algorithms, acting like legal hackers, and were invited to share their skills and experiences with the community. So, manufactures changed their habits to reject the possibility to reveal flaws in their systems and choose an ethic approach to improve the worldwide knowledge. Also manufacturers that produce IT systems for pharmaceutical companies must consider the opportunity to look for new devices to protect all sensible data regarding the clinical study. Indeed, personal details of patients contained in clinical study are usually shared between centres involved in the trial and become more sensitive of possible attacks. Thus, it’s ethic that these data should be preserved.

RFID to easily identify frozen samples

RFID means radio-frequency identification and is used to define tagged object that can be recognized through radio-waves. This system is composed by two part: the first one is an integrated circuit in which is possible to store and process information and modulate and de-modulated radio frequency; the second part is usually an antenna required for receiving and transmitting the signal. The first use of RFID was during the II World War when allies used this system to distinguish their planes from those of enemy; then in 1973 it was US patented by Mario Cardullo with a business plan showing uses in transportation, banking, security and medical. Now, RFID technology is currently used for several application: from passport to animal identification, from race timing to transportations payments.

In healthcare RFID are undergone to severe regulation to defence the privacy of consumers. In 2006, Food and Drug Administration highlighted the importance to do not include information about consumers, health practitioners or other uses of the product out of label. The RFID tag may be covered with a seal containing a logo, a message unrelated to product and an unique serial number and, mostly important, the tag will not substitute the traditional labelling process. This point wasn’t observed by GSK when they used RFID tag to control HIV treatment capsules and for this reason a violation was signalled. Another important use in scientific world is the tracking of nuclear substances during both storage and transportation. Indeed, scientists from the Department of Energy Argonne National Laboratory set up a system in order to gain information about the nuclear materials in real time, allowing the constant monitoring of the materials self. Moreover, some RFID devices have been added to notebooks to streamline information management and retrieval. This tool could be useful in big pharma, or big institutions in order to correctly manage all information without loosing time.

Sample identification is another important application in the scientific laboratory; for instance, it could be really useful to recognize frozen samples –cells, proteins and RNAs- without opening the box. The great advantage of this system is the perfect preservation of biological materials, indeed everyone knows that continuous and repeated extraction from liquid nitrogen seriously damage biological samples. Furthermore, RFID allows to immediately control the box status and find if vials are missing. In quality control system this system is strongly recommended because it makes transparent audit process. Modern RFID technology is miniaturized and cheap, so it could be applied on each cryovials through self-adhesive cryo safe labels. Using RFID tags has a lot of advantages specially if the freezing service is centralized or common for several laboratories: not only box contents are always well described, but also operators’ mistakes can be immediately repaired without loosing precious materials. Also in small scale laboratories this system could have some applications to manage samples during years specially if there is a quick turnover of workers, as usually happens in academic labs. RFID system is a modern tool to facilitate scientific job.

Tools to manage the bibliography

Bibliography is a fundamental part of every scientific publication, from PhD thesis to review and experimental paper, as well as pharmaceutical reports or clinician case reports. Each journal has specific requirements and before starting writing any documents it could be useful know about bibliography rule.
In particular, in scientific paper every sentence must refer to other publications in order to prove that the work has been founded on scientifically accepted basis. References can be managed through several software, for instance EndNote. Nature website proposes a new tool to manage references, called Connotea. This tool allows saving links to web pages or PubMed entry numbers or Amazon pages for a book. Because Connotea it web-based, it’s not necessary to download references and bibliography is always available in each computer. Furthermore, it’s also possible to share references with colleagues or everyone is interested, and there are no limitations about the number of persons with which share these information or about the number of link saved. To use Connotea you must subscribe for free and you will get your space in which you can tag your reference and easily recognize them. Knowing literature is the first step to produce significant data in science!

LIMS and stem cell research

LIMS is an acronym for Laboratory Information Management Software, is a common software used in environmental, pharmaceutical and research institutions. It’s a software to manage laboratory life, indeed with this tool it’s possible not only to manage samples and standards, users and instruments, but also to send invoices, control the automation of the workflow, manage projects. The current goal is to retain result achievement, elaboration, further decision and final review directly at the workplace, and not in the office. Indeed, all laboratory users can login and use this software, projects are organized by type, subtype, priority and other criteria and all information related are recorded within; moreover, also instruments can send data directly to LIMS that is configured to guarantee the traceability of the work. With LIMS it’s possible to save time and money and improve rate and productivity: indeed, big inventories could be reduced or eliminated at all and researchers don’t waste too much time to search data of previous experiments and so on.

Stem cell research is an exciting branch of science that quickly advances and provides data. In order to manage these data and facilitate the collaboration between institutions it could be reasonable the use of LIMS in the most upgraded version. The first feature that the software should have is to be user friendly because in one laboratory researchers could have different background and this difference could be more significant in more laboratories during a collaboration. In order to communicate results or change samples or make common decisions, a software like LIMS 247 used in all labs could help to coordinate the work. Many techniques and protocols can be applied in stem cell research, from cellular biology to molecular biology to biochemistry; the use of special software, directly configured by researchers, can help to record workflows and data and trace them: this is the second important feature of a software that should be used in stem cell research. Progress reports are also important during laboratory life, LIMS guarantees a secure mechanism for data reporting, always checked by the quality control system present in the software. We have presented one possible application of LIMS in research laboratories, but this software could be successfully employed also for the management of cell cultures and patients samples collected in hospitals. Again, to perfectly recorded every information about each sample -and when we work with patients the perfection is a must- it’s possible to use LIMS. This software can help researchers to maintain the traceability of the samples and clinicians that can base their decisions on scientific data from the same samples. This process could improve the results from regenerative medicine, in the case of stem cell research, but in all clinician departments could give a great hand. Modern science, specially stem cell research that is the future for medicine and biology, cannot exclude informational tools from its life: software like LIMS 247 from RURO Inc. could improve the quality of scientific works and increase the data and publications productivity and the quality of the clinical services for patients.

Challenging on data management

Data management is a crucial aspect of scientific work, not only to correctly collect and retrieve information, but also to constantly have a complete vision of the work. In quality control system, data are classified by a code, defined by scientists and common for all laboratory members. For instance, files can be named with date, operator, project and kind of experiment: in this way it’s possible to identify one file without loosing time to check all folders and open every document.

Otherwise, it’s possible to use special software that is commercially available to manage your data. In lab research different kind of data can be generated: firstly raw data, such as numbers, pictures or texts (for example patient interview in clinical studies). Raw data have to be conserved, retrievable and in some cases protected by password, especially in clinical studies when sensible information about patient’s health are collected. These data can derive from several instruments that work with their specific program: they have to be converted in a unique format in order to be useful for elaboration. Raw data are usually resumed in graphs or tables that can immediately and communicate the result from complex experiments. At this point, it’s crucial to choose the best way to communicate results and valorize your work. Indeed, few graphs and table in scientific article have to present a long work made by several scientists in some cases. A correct data management system is useful during article writing to retrieve all important information and it’s cost- effective because avoid to loose time in searching raw or elaborated data or in repeating experiments those data are missing.

Not only in laboratory research, but also in clinical trial is important to correctly manage data for different reasons: firstly in clinical trials data often derive from patients and are subjected to privacy law, secondarily a really large amount of data are usually produced, especially during latest phases of trial when thousand patients are enrolled, lastly clinical trials are expensive and correctly managing data decreases costs. Data management software is feature-rich and includes planning, preparation and performance rather than raw data collector. Moreover, scientist contact information, deadlines, milestones and progress report have to be available to allow a complete overview of the project. The software is usually used in different centers around the world because clinical trials involve several institutions and must be user-friendly and verified from external intrusion.

In conclusion, data management is a challenging aspect of modern science for many reasons: data generated from research or clinical studies are a huge amount and often derive from different institutions that collaborate: this means that coordination between centres in data collection is essential; moreover, data are conserved and protected in respect of quality control standard and privacy law, respectively. Modern and efficient software is available now, and in next future it’s necessary to further customize IT products in order to make data management easier and less expensive.

How to design a high-throughput screening

The correct design of a high-throughput screening is essential to obtain great results and save time and money. Eighty years ago, Ronald Fisher published his theory about experimental design. He developed a mathematical framework in which interactions among different experimental factors are surveyed in order to identify the optimal conditions.

Fisher’s method, called DoE (The Design of Experiments) has been applied in many branches of life sciences, such as enzymology, structural studies, biochemistry. Several software are now available, based on this approach: for instance at the University of Massachusetts they adapted commercial DoE software for enzyme assay development in automatic liquid handling platform and used a special reader to analyse the results. They identified the important interactions between assay components –pH and salt concentration- that could interfere with enzyme activity. At Umetrics – New Jersey- DoE software is used for both the initial screening and follow-up optimisation experiments. Firstly, they found the most important variables, then used data generated to train a system to stay within an optimal range for the screening. The main challenge in first use of DoE software is integration with automation; once overcame this obstacle, high-throughput screening could be performed. Biotech and pharmaceutical companies already use DoE method, maybe in some years also academic world will currently adapt this approach.

Advances in microscopy

Microscopy is an essential tool to observe cells and catch a picture of cellular behaviour in response to peculiar stimuli. In last number of Nature, five new microscopes have been described. These technologies could allow us to observe details once visible with electron microscope with light, or to use thick sample in electron microscopy instead of light microscopy.
Of course, these instrumentations are really expensive and so sensible that can easily generate artefacts, if mistakes are made. Scientists need a complex training not only for use these microscopes, but also to correctly understand images resulted. For this reason, it becomes important the presence of computational biologists and engineers in research group, to obtain consistent results. But more important, is the collaboration between groups in universities and institutions, in order to buy and maximally use these instrumentations. Rather than shared instrumentation, molecular and cellular biologists need to share their output images in one common database. A repository could make images available for all, and help to better elaborate them. An example of such framework was launched last year by the Journal of Cell Biology: the scientific community’s support will make updated and accessible this important tool.

Reference: Nature vol 459, issue 7247, 4 June 2009
http://jcb-dataviewer.rupress.org/