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!

Application of molecular biology to medicine

Modern medicine is based on evidence. Despite few years ago, physicians based their diagnosis and therapies on their previous experiences, now clinical trials, approved protocols and worldwide accepted treatment help physicians to make the better choice for their patients. To reach this important goal, molecular medicine gave a big contribution. Molecular medicine is a novel branch of medicine in which molecular biology or biochemistry techniques are usually used to accomplish exams and screening or diagnose the diseases. Molecular biology labs have worked as research and development department to improve protocols or set up novel methodologies at the beginning just to be used for research purposes, then applied to diagnosis. For instance, we could focus our attention on the polymerase chain reaction, namely the PCR.
This techniques has been developed to produce DNA portion in vitro and has quickly revolutionized molecular biology, allowing cloning, sequencing and in general gene manipulation. The improved type of PCR, the real time PCR is now currently used in modern hospital to detect certain diseases, such as recidivate leukemia in patients’ blood or gene signature in familial diseases. Other important tools which have found a good application in diagnosis are the monoclonal/ polyclonal antibodies. Several techniques employed antibodies to detect proteins in cellular lysates through western blotting, or directly in whole cells, through the immuno-chemistry and molecular imaging. As well as, it’s also possible to purify small amount of native protein through immuno-precipitation and so on. Antibodies are really largely used in biochemistry labs and some techniques are applied also in diagnostic labs.
For instance, we can talk about the ELISA assay, normally used to quantify serum proteins or cell sorting analysis, in which some antibodies that specifically recognize surface proteins are used to separate different kind of cells. Finally, also cellular biology gave important results in modern medicine. The capability to culture in vitro cellular populations changes the therapeutic opportunity for a lot of diseases. For instance, now it’s possible to select healthy cellular population in leukemic patient, propagate it in vitro and then draft it, reducing in this way several problems of rejection and immuno-suppressive events. We can continue to talk about other examples of molecular, biochemical or cellular protocols that have found a great application in clinics. This overview strongly confirms how scientific advances are important because they have an immediate benefit on modern medicine and as a consequence on the human life. It’s important to remember that not only good protocols, but also good quality of science and good data management and reporting are two further parameters to improve modern medicine, but this is the topic for another post!!!

Automation in High-throughput screening

Drug discovery uses the major amount of its resources for the high throughput screening. Based on specific probabilistic calculation, large experiments in HTS are performed by pharmaceutical and biotech companies to identify some molecules that could become drug after further long analyses. Robots are usually used in this complex process. It’s important that all data are generated in reliable and accurate manner in order to obtain useful results.
Robots can execute some passages: from serial dilution to reaction buffer disposal. In each of these steps, errors could be generated and, giving the small volumes in which HTS is usually performed, robots must be well calibrated in order to exclude the possibility to have this kind of problems. A lot of data arises from an HTS. Data management and statistical analyses are other key- steps for the high throughput screening. Thus, IT systems have not only to control robots to correctly work, but also help scientists to produce meaningful results from raw data. This kind of experiments are highly expensive and can be repeated only strictly necessary times. However, it’s really important to plan the experiment in the correct way and set up robot ant other IT systems involved into the process to obtain more data as possible.

Challenging in food safety

Food safety is one of most important challenge in our countries. Indeed, adulteration and poising food are often described in newspapers. FDA and ESFA are the organisations issued to guarantee food safety in U.S and Europe, respectively. Which are the most common problems that determine food adulteration. The first cause of this kind of problem is the bacterial contamination: indeed bacteria can provoke food spoilage as well as they are pathogen in some cases.

To decrease the possibility of food spoilage, numerous testing must be performed in food processing company. The safety ideal “from farm to fork” created by FDA can be reached only through an attentive analysis of raw materials, processing and packing procedures in order to assure maximal sterility in each step. Furthermore, some laboratories are specialised in bacterial, toxin and sterility testing: the common goal is to provide consumers with safe and wholesome food at least for all shelf-life of food self. These laboratories usually offer a broad range of services and usually communicate with their clients through LIMS system. LIMS systems, indeed, are able to collect large number of data analysis, reports and general forms and rapidly make them available to clients.

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.

Critical points of medical writing

An important part of clinical studies is often associated to write report, analyze data and do statistics. Commercial software are now available to facilitate data collection and management and the collaboration between institutions, but one difficult work still be the elaboration of the results and the creation of final report to be presented to approval committees. Thus, medical writing department assumes crucial role in a pharmaceutical company. This department must be organized in order to efficiently accomplish the production of promotional materials, documentation for marketing new products and manuscript for publication. Medical writing follows specific guidelines to guarantee scientific correctness and ethical standards. Indeed, results reported in papers, reviews and brochures must be rigorous, transparent and consistent; the writing must be comprehensible, accurate, concise and logically organized, all the assertions must be justified and proper terminology facilitates the proficiency. Medical and nursing professionals often don’t have time or inclination to write their papers, as well as in pharmaceutical companies results from unsuccessful clinical studies are not published again because of lack of time.

It’s astonishing that a large percentage of works presented in national meetings doesn’t proceed to publication in peer review journal. In this way the advances of science are avoided. Fortunately, professional medical writers can supply the important service to write papers and reviews and make these data available to scientific community. Medical writer are often ghost- writer and their name doesn’t appear between authors in the final publication, even if now a task force of European medical writer association (EMWA) tries to solve this problem. For transparency, indeed, the reader should always know about the presence of a ghost-writer and also the name “ghost-writer” itself is misleading; EMWA task force suggests the use of a more neutral term. Anyway, medical writing still stimulating and interesting work, because allows to enter in direct contact with clinical researchers and know results of studies before the publication itself. Not only physicians and scientists must be responsible of data truth, but also medical writer must learn about ethical practice: in this way, papers are really scientifically correct and scientific literature continues to have a significance. Furthermore, founding and grant achievement are often associated to the number and quality of publication of the principal investigator, so writing numerous papers represents an opportunity also to obtain financial advantages, rather than scientific. Publishing results allows to receive feedback about your study and useful suggestion for future perspectives and, in some cases, to create a network of common interest with other groups that work at the same topic. In conclusion, medical writing is one new aspect of scientific and pharmaceutical life that guarantees success of studies, but also could be considered a new profession with specific rules, aims and challenges.

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.

Quality control in lab

Quality control in laboratory is essential to obtain great results. Several studies demonstrated that more publications are accepted by peer reviewed journals when good laboratory procedures are followed. This means that giving the same time and the same amount of money, labs that work with GLP are more productive than those that aren’t in GLP. Good laboratory procedures are rules (SOPs) which scientists have to keep in mind when they perform experiments and have to be the same for all people working in the lab.

Standard operating procedures (SOPs) should be written for each instrumentation present in lab and represent guidelines to work with. From calibration to final cleaning, terms of use of an instrument are well described in order to guarantee firstly that instrument is correctly used, secondarily that everyone in lab uses machine in the same manner: this is a crucial point to allow comparison of results produced in lab. A training has to be done before using an instrument, at least the first time with a manufacturer’s specialist and then by the most expert person in lab. Each instrument has a responsible that takes care of management and maintenance. Ideally, in this way measurements obtained from an instrument by all users are comparable and consistent and standard deviation between repeated experiments should decrease. SOPs are not applied only to instruments use, but can also describe other important actions, normally performed in lab. For instance, when data management has well defined rules, it’s easier and faster to retrieve information. Whatever kind of data elaborated in files –texts, tables, pictures, graphs- should be classified and named with a code that, for instance, contains project number, operator, day, kind of file: so just reading the name, it should be possible to understand if we have found what we are looking for. Standardization of data management is crucial when there are a lot of people in lab or there is a quick turnover, indeed these are common cases in which some data could be lost. Writing a notebook is another part of scientific work that is essential for scientist and also this aspect has to be standardized. Indeed, in notebook protocols are usually described, raw data collected, first observations noted and each scientist tends to personalize his book.
A standardized manner of writing notebook is important to make easier sharing protocols and ideas between group members. Last but not least, all reagents from salts to enzymes, from culture media to animals, have to be registered in terms of availability, arrival date, expiration date in a common repository accessible to all people working. In this way, scientists can quickly check to have all reagents for their experiment before starting and don’t waste time and, more important, they don’t waste money to buy reagents maybe already available in lab, but hidden in some dark corner. Software is available to correctly manage all kind of scientific repository, from freezers to nitrogen tank to collect cells. In conclusion, following GLP makes experimental work more efficient and less expensive.