Bioinformatics - Wikipedia As R is used in an interdisciplinary field, a computer scientist might want to start with genome biology and a biologist with R programming. ELET 2300 - Introduction To C++ Programming Credit Hours: 3 (Note: Students may choose either ELET 2300 or BTEC 2322 as an elective, but they must complete 3 courses at the 3000 or 4000 level for minor.) Its always better to know more advanced languages such as Java. It always helps if you diversify your skillset. The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. The speed of processing was timed using the GNU program 'time' which is present in most of the Linux distributions. Simulation of Folding Kinetics for Aligned RNAs. sharing sensitive information, make sure youre on a federal To provide the best experiences, we use technologies like cookies to store and/or access device information. The biggest drawback for semi-compiled languages is their memory usage, since they required about 20 times more memory than C and 3 times more memory than Perl (Fig (Fig44). A minimum GPA of 2.00 must be maintained in all biology courses and in the combined co-requisite courses. The https:// ensures that you are connecting to the Perl clearly outperformed Python for I/O operations. The Graduate Program in Bioinformatics offers the Master of Science [MS] degree, with a curriculum created to prepare students for the most cutting-edge industrial positions in the field. Program Overview As the healthcare, biotechnology, and pharmaceutical industries become more reliant on complex data analysis and artificial intelligence, the need for experts with both biological knowledge and programming and quantitative skills will continue to increase. The performance of C and C++ was very similar (Fig (Fig1,1, ,2,2, ,3,3, ,4).4). Factors such as performance and memory usage are important, but need not be the sole determinant when choosing a language. The STRING Database in 2021: Customizable ProteinProtein Networks, and Functional Characterization of User-Uploaded Gene/Measurement Sets. The R Language: An Engine for Bioinformatics and Data Science The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Ankita worked as a Data Curation Intern at NuGenomics. Basic Local Alignment Search Tool. What will I learn in Brandeis GPS's Bioinformatics program? There is, at present, little direct data on the underlying speed and efficiency of equivalent algorithms written in different languages. My Journey Into Data Science and Bioinformatics Part 1: Programming The test program made use of input streams and regular expressions. The way objects are accessed and stored in memory influences the performance of each language. Background: Researchers and medical scientists in academia who have extensive knowledge in quantitative fields like mathematics and statistics also learn and work with R to analyze genomic data. Mol Biol Evol. This process is repeated until two nodes are separated by one branch. Raghava GPS, Searle SMJ, Audley PC, Barber JD, Barton GJ. All authors read and approved the final manuscript. R is used by many programmers and scientists for data analysis, machine learning, and statistical inference. and transmitted securely. -, McGuffin LJ. A Quick Guide for Developing Effective Bioinformatics Programming In this example a two-dimensional matrix is used to store the highest scores with the top left corner representing the beginning of the sequences and the bottom right corner representing the end of the sequences, which is the starting point of the alignment. See this image and copyright information in PMC. Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Regnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. Assessing computational tools for the discovery of transcription factor binding sites. Dynamic programming (DP) is a most fundamental programming technique in bioinformatics. Clipboard, Search History, and several other advanced features are temporarily unavailable. Federal government websites often end in .gov or .mil. Memory usage comparison for the Neighbor-Joining and global alignment programs implemented in C, C++, C#, Java, Perl and Python. * CHEM 0110 - GENERAL CHEMISTRY 1and CHEM 0120 - GENERAL CHEMISTRY 2are pre-requisites to taking CHEM 0310. I was a newbie to this fascinating programming language but, unfortunately, R was not included in my curriculum. On Windows, a simple Perl script launching the programs with the option -Dprof was used to time all processes. There were several reasons for this benchmarking exercise. The most computer intensive component of this program is the pairwise comparison used to compute the dissimilarity matrix. GitHub. This difference did not arise through any inability of C# to handle large files, since it read these files faster than Java did. During the benchmarking process, unnecessary services were disabled. It is worth noting that the Perl implementation of the NJ algorithm was substantially improved by converting each sequence to an array instead of using the substr function on the string of characters for computing the similarity matrix. Becoming A Data-Driven CEO|Domo. Accessibility Learning bioinformatics will not only help you construct algorithms and pipelines but will also help in understanding biological problems from a computational perspective. sharing sensitive information, make sure youre on a federal Interestingly, Java was slightly faster in the global alignment program (Fig (Fig1)1) but much slower in the NJ program (Fig (Fig2).2). This helps the learners to rectify their mistakes and score better marks. Program Statistics Admissions Requirements for the Graduate Major in Bioinformatics APPLYING After exploring options and choosing a specific program, follow the steps on our University's graduate application process: Steps to Apply General application process for all UCLA Graduate Programs PHONE (310) 825-0068 EMAIL However, it is possible that the same program, written in different languages, or running under different operating systems, may exhibit significant differences in speed and efficiency. Programs in these languages generally contained more lines of code. So, what exactly are programming and coding? [(accessed on 21 April 2022)]. C# and Java have a higher memory-size penalty for objects than other object oriented languages such as C++ due to their ability to use reflection. This item: Bioinformatics Programming in Python: A Practical Course for Beginners. Next-Generation Sequencing Bioinformatics Pipelines - AACC Advantages of Python Programming in bioinformatics. All biology courses taken for the major must be completed with a C or better. A typical bioinformatics program reads FASTA files, holds the DNA sequences in memory, performs different computing tasks on the sequences, and finally writes the results to a file. Comprehensive Perl Archive Network (CPAN). Motivation: Transition your career with a degree in Bioinformatics But, coding opens up several possibilities to understand different organisms, different conditions, and different systems. In the test example 76 Hantavirus segment L sequences were used with an overall alignment length of 6580 nucleotides. In the field of bioinformatics, Python programming provides several benefits. Large amounts of data can be generated in different formats. The R programming language is approaching its 30th birthday, and in the last three decades it has achieved a prominent role in statistics, bioinformatics, and data science in general. Nevertheless, a noticeable difference was observed (Fig. PMC Role of Programming (R & Python) in Biotech and Medicine The nodes of the tree were implemented as structures in C and C++, as objects in C#, Java and Python and anonymous hash tables in Perl. Our program did not aim to compare the regular expression performances of each language but the overall speed of such a task. Rahimi I., Chen F., Gandomi A.H. A Review on COVID-19 Forecasting Models. Please enable it to take advantage of the complete set of features! Profiling was also used to inspect the time repartition and memory allocation. But, programming and coding are the foundations for anyone who develops software and works with data. The standard library diversity and size of Java, Python and C# are a major advantage compared to the other languages,. For example, the core of the NJ program was written in Perl, but when the subroutine calculating a pairwise comparison was written in C, it sped up the program from 11.8 seconds to 0.29 seconds. Speed comparison of the BLAST parsing program. https://creativecommons.org/licenses/by/4.0/, https://cran.r-project.org/bin/windows/base/, https://www.rstudio.com/products/rpackages/, https://cran.r-project.org/web/packages/policies.html, https://www.bioconductor.org/packages/release/BiocViews.html, https://projects.eclipse.org/projects/science.statet, https://github.com/REditorSupport/sublime-ide-r, http://topepo.github.io/caret/available-models.html, https://shiny.rstudio.com/articles/reactivity-overview.html, https://www.rstudio.com/products/shiny/shiny-server/, https://www.routledge.com/Chapman--HallCRC-The-R-Series/book-series/CRCTHERSER, https://www.r-project.org/other-docs.html, https://www.mdpi.com/article/10.3390/life12050648/s1, https://hypatia.math.ethz.ch/pipermail/r-help/, https://cran.r-project.org/doc/html/interface98-paper/paper.html, https://cran.r-project.org/doc/FAQ/R-FAQ.html#What-are-the-differences-between-R-and-S_003f, https://stat.ethz.ch/pipermail/r-announce/1997/000000.html, https://stat.ethz.ch/pipermail/r-announce/1997/000001.html, https://www.r-project.org/contributors.html, https://stat.ethz.ch/pipermail/r-announce/1999/000103.html, https://stat.ethz.ch/pipermail/r-announce/2000/000127.html, https://stat.ethz.ch/pipermail/r-announce/2003/000385.html, https://www.r-project.org/foundation/Rfoundation-statutes.pdf, https://www.r-statistics.com/2013/04/r-3-0-0-is-released-whats-new-and-how-to-upgrade/, https://blog.revolutionanalytics.com/2020/04/r-400-is-released.html, https://www.bioconductor.org/about/annual-reports/AnnRep2002.pdf, https://qz.com/1007328/all-hail-ggplot2-the-code-powering-all-those-excellent-charts-is-10-years-old/, https://rstudio.comhttps://www.rstudio.com/blog/rstudio-new-open-source-ide-for-r/, https://www.r-bloggers.com/2012/11/rstudio-releases-shiny/, https://www.jumpingrivers.com/blog/parquet-file-format-big-data-r/, https://usermanual.wiki/Document/A20guide20to20Eclipse20and20the20R20plugin20StatET.1831954166, https://marketplace.visualstudio.com/items?itemName=Ikuyadeu.r, https://insights.stackoverflow.com/survey/2021#section-most-popular-technologies-integrated-development-environment, https://github.com/jhallen/joes-sandbox/tree/master/editor-perf, https://blog.revolutionanalytics.com/2014/03/emacs-ess-and-r-for-zombies.html, https://www.northeastern.edu/graduate/blog/most-popular-programming-languages/, https://github.com/Rdatatable/data.table/wiki/Benchmarks-%3A-Grouping, https://www.rebeccabarter.com/blog/2020-03-25_machine_learning/, https://docs.h2o.ai/h2o/latest-stable/h2o-r/docs/index.html, https://cran.r-project.org/web/packages/prophet/index.html, https://www.domo.com/solution/data-never-sleeps-6, https://www.statista.com/statistics/617136/digital-population-worldwide/. Python was the worst performer for parsing a BLAST file (Fig (Fig3),3), taking more than 38 minutes to process the file compared to Perl, which took only 7.28 minutes. BTEC 3317 - Biotechnology Regulatory Environment Credit Hours: 3.0; BTEC 4300 - Principles of Bioinformatics Credit Hours: 3.0 Epub 2010 Aug 25. With the advent of emerging technologies, strong programming skills are needed to deal with a massive amount of biological data. Whereas Perl gives more freedom to the programmer resulting, in some cases, in programs that are unreadable for non Perl programmers. 2017 Oct;109(5-6):419-431. doi: 10.1016/j.ygeno.2017.06.007. The Perl Compatible Regular Expression [20] library was used for C and C++ since their standard library does not implement built-in regular expressions. To read such a large file and overcome the 2 GB file size limitation the flags "-D LARGEFILE_SOURCE -D_FILE_OFFSET_BITS = 64" were used when compiling the C and C++ source code. 8600 Rockville Pike In this paper we will refer to ease of coding as the number of coding lines needed to write a program, taking into account the availability of libraries, which is a factor in the number of coding lines needed for compiling a program. It is a continuously evolving language with upgrades and updates on the R packages frequently. A comparison of common programming languages used in bioinformatics An integral component of setting up a bioinformatics program for research, training, or service purposes is access to computational resources. Learning R programming will open the door to opportunities or career paths that the high school students might want to take up. R was adopted by the bioinformatics community throughout the past years as the top . Learning the basics of R can help the students relate their knowledge to the codes they write and also compare the output of the code with the solutions of their calculations. Wang H, Wang J, Zhang L, Sun P, Du N, Li Y. Int J Biol Sci. The best choice of language for a task would be according to the original philosophy, keeping in mind that Java is portable web oriented language, Perl is a powerful script language, Python is an easily coded language and C and C++ are efficient languages used in operating systems and drivers. Intro to R and RStudio for Genomics: Summary and Setup - Data Carpentry Honors in Bioinformatics is granted if, in addition to fulfilling all requirements for the major, the student: Nondiscrimination and Anti-Harassment Policy, MATH 0220 - ANALYTIC GEOMETRY AND CALCULUS 1, MATH 0230 - ANALYTIC GEOMETRY AND CALCULUS 2, PHYS 0174 - BASIC PHYSICS, SCIENCE AND ENGINEERING 1 (INTEGRATED), PHYS 0175 - BASIC PHYSICS, SCIENCE AND ENGINEERING 2 (INTEGRATED), BIOSC 0057 - FOUNDATIONS OF BIOLOGY RESEARCH LABORATORY 1, BIOSC 0067 - FOUNDATIONS OF BIOLOGY RESEARCH LABORATORY 2, CHEM 0330 - ORGANIC CHEMISTRY LABORATORY 1, CHEM 0340 - ORGANIC CHEMISTRY LABORATORY 2, BIOSC 1810 - MACROMOLECULAR STRUCTURE AND FUNCTION, CS 0401 - INTERMEDIATE PROGRAMMING USING JAVA, CS 0445 - ALGORITHMS AND DATA STRUCTURES 1, CS 1501 - ALGORITHMS AND DATA STRUCTURES 2, CS 0007 - INTRODUCTION TO COMPUTER PROGRAMMING, BIOSC 1640 - COMPUTATIONAL BIOLOGY RESEARCH, BIOSC 1820 - METABOLIC PATHWAYS AND REGULATION, BIOSC 1950 - MOLECULAR GENETICS LABORATORY, CS 1520 - PROGRAMMING LANGUAGE FOR WEB APPLICATIONS, CS 1571 - INTRODUCTION TO ARTIFICIAL INTELLIGENCE, CS 1645 - INTRODUCTION TO HIGH PERFORMANCE COMPUTING SYSTEMS, CHEM 0250 - INTRODUCTION TO ANALYTICAL CHEMISTRY, STAT 1311 - APPLIED MULTIVARIATE ANALYSIS, Graduate School of Public and International Affairs, Kenneth P. Dietrich School of Arts and Sciences, School of Health and Rehabilitation Sciences, University Center for International Studies, University Learning Research and Development Center, Administrative Officers, Schools, and Campuses, Acalog Academic Catalog Management System (ACMS). Perl emphasizes support for common application-oriented tasks, by having built-in regular expressions, file scanning and report generating features. 966 ratings. Surprisingly, Java performed better than Perl during the regular expression benchmark. Where You can Learn about R Programming for bioinformatics? PhD Students attain a common core of knowledge, with emphasis on their ability to integrate biological and mathematical disciplines. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found. 2018 May 22;14(8):901-906. doi: 10.7150/ijbs.24327. In Perl, a unique statement can be used to detect a pattern and the captured pattern is retrieved with the special variable $1, whereas in Java the programmer has to instantiate a Pattern object which is a compiled representation of the regular expression, then create a Matcher object which performs match operations on a character sequence by interpreting the pattern object. Biomed Res Int. As R provides a number of statistical packages and libraries, it is favorable for analysis in the field of bioinformatics and genomics. Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies. PeerJ. To learn programming as a life science or biotech student can be a complex task at the beginning. The number of lines in a program varies from one programmer to another, and also on their willingness to shorten the code to the detriment of readability. Memory usage comparison of the Neighbor-Joining and global alignment programs. Surprisingly, you can even apply the concepts learned from R to many programming languages like Python. For example, numerous Gene Ontology [19] programs use BLAST outputs to assign GO terms to unknown sequences. Zdobnov EM, Apweiler R. InterProScan an integration platform for the signature-recognition methods in InterPro. 2022 Apr 22;10:e11683. 2022 Jan 9;13(4):1145-1159. doi: 10.7150/jca.63635. -, Irizarry RA, Wu Z, Jaffee HA. R is predominantly used for statistical computing and graphics. The Sellers algorithm is a simple global sequence alignment method using a dynamic programming approach with a gap penalty. Available online: Papacharalampous G.A., Tyralis H. Evaluation of Random Forests and Prophet for Daily Streamflow Forecasting. Four credits of undergraduate research are required for the major. BIOSC 1640and CS 1640satisfy the bioinformatics major capstone experience requirement. Bioinformatics allows and encourages the application of many different parallel programming approaches. These quick scripts are usually implemented in Perl or Python. The programs were run on Linux and Windows platforms. including sets of classes to create graphical interfaces, data structures (vectors, hash tables, stacks, queues), regular expression, database access and networking. Bioinformatics | UCLA Graduate Programs BLAST, Basic Local Alignment Search Tool; CGI, Common Gateway Interface; CPAN, Comprehensive Perl Archive Network; CPU, Central Processing Unit; DNA, Deoxyribo Nucleic Acid; FASTA, FAST-All; GI, Geninfo Identifier; GO, Gene Ontology; I/O, input and output; JNI, Java Native Interface; JVM, Java Virtual Machine; NJ, Neighbor Joining; SNP, Single Nucleotide Polymorphism; XS, eXternal Subroutine. Bioinformatics is indispensable and is a promising path to professional success. Introducing R programming to high school students will teach them how to think about code and will directly impact their future careers. The most widely used libraries are BioPerl, BioPython and BioJava. Barter R. Tidymodels: Tidy Machine Learning in R. [(accessed on 8 December 2021)]. Savings in computing time will be essential for such analyses to be efficient. MeSH Introduction to programming for Bioinformatics with Python - Udemy BLAST is a tool calculating sequence similarities between a query sequence and sequences lodged in a specially formatted database. Mathematics and statistics are popular among high school subjects. Ten simple rules for developing bioinformatics capacity at an - PLOS David C. Frederick Honors College equivalents for any of the above courses are accepted. If we consider that Perl was nearly 60 times slower than C in the global alignment benchmark and that a query sequence of 3500 nucleotides against the non-redundant database took roughly 10 seconds (including the transfer over the web), then if the query is submitted a million times during the day, the total computation time would have increased 60 fold, taking considerably more server time. In this paper we examined three commonly used tasks in biology, the Sellers algorithm [9] the Neighbor-Joining NJ algorithm [10] and a program parsing the output of BLAST [11]. Unable to load your collection due to an error, Unable to load your delegates due to an error. 1624 May 2015; pp. Motivation: Dynamic programming is probably the most popular programming method in bioinformatics. Biologists and biotechnologists need programming skills too. [(accessed on 21 April 2022)]. Another common task in bioinformatics is text mining or text parsing. Students interested in departmental honors should contact department advisors for information. The technical storage or access is strictly necessary for the legitimate purpose of enabling the use of a specific service explicitly requested by the subscriber or user, or for the sole purpose of carrying out the transmission of a communication over an electronic communications network. VDOM DHTML tml>. Understanding how to collect, study, and analyze biological data is a useful skill in a variety of careers and industry areas. Advising for Bioinformatics majors is housed in both the Department of Biology and the Department of Computer Science. Speed comparison of the global alignment algorithm using a gap penalty of 10 implemented in C, C++, C#, Java, Perl and Python. She completed her Bachelors & Masters in Biotechnology and interned at CSIR, Pine Biotech, and Guwahati Biotech Park. Java regular expression implementation appeared to outperform C# (Fig (Fig3).3). Mangalam H. The Bio* toolkits a brief overview. But, for a young biotechnologist or life scientist to work at cutting-edge research require rapidly evolving technologies and huge biological datasets for which solid programming and statistical skills are necessary to be productive. Co-requisite courses must be taken in chemistry, physics, and mathematics and/or statistics, as follows. Pal S., Mondal S., Das G., Khatua S., Ghosh Z. I loved programming since my undergraduate days. Statistical Genomics: Methods and Protocols. Mercatelli D., Triboli L., Fornasari E., Ray F., Giorgi F.M. Available online: Clough E., Barrett T. The Gene Expression Omnibus Database. 2022 Apr 27;12(5):648. doi: 10.3390/life12050648. If a C-or lower is earned in an elective course for the major and is not repeated, the course will be used to calculate the overall GPA but will not be counted toward the 32 credits required for the major. The same observation would apply for the memory usage. A comparison of common programming languages used in bioinformatics Hence no hashtable was used in this benchmark. http://creativecommons.org/licenses/by/2.0. In the first half of the course, we investigate DNA . Perl was three times as fast as Python when reading a FASTA file and needed half of the space to store the sequences in memory (Fig (Fig4).4). If you are aiming for a research career in academia, expertise in any one of the programming languages is valuable for your research work. Scores for aligned characters are computed (see equation 1) and stored in a similarity matrix F with a linear gap penalty d, and where s(i, j) is the substitution score for character i and j. The major is designed to meet the increasing demand for trained people in this emerging area, which crosses the traditional fields of biological . Surprisingly, the field of Bioinformatics serves as an intersection in this aspect. Comparison of Affymetrix GeneChip expression measures. The program parses and prints in a one line comma separated file, the name of the sequence, containing the gene identifier, bit score, identity percentage, e-value and positive matches. Parallel Programming in Bioinformatics: Some Interesting - Springer Clegg AB, Shepherd AJ. {"type":"entrez-nucleotide","attrs":{"text":"AJ005637","term_id":"3861465"}}, {"type":"entrez-protein","attrs":{"text":"ABD75716","term_id":"89515715"}}. Given the rapid improvements in high throughput sequencing technologies, it is likely that tests involving orders of magnitude more sequences will be conducted in the future. PMC Number of lines for the global alignment, BLAST parser and Neighbor-Joining programs implemented in C, C++, C#, Java, Perl and Python. The technical storage or access is necessary for the legitimate purpose of storing preferences that are not requested by the subscriber or user. Bioinformatics Specialization (UCSD) | Coursera For large-scale data analysis, understanding statistics is a prerequisite. Sun is constantly improving the Java compiler and interpreter and other JVM implementations are also available such as Kaffe [18] and IBM's. 1994;11:459468. C and C++ are fully compiled languages, suitable for system-intensive tasks. BMC Bioinformatics. In the NJ (Fig (Fig2)2) and the BLAST parser (Fig (Fig3),3), C and C++ were both slower on Windows whereas on Windows, Java and Perl were faster in the NJ example (Fig (Fig2)2) but slower in the BLAST parser example. In this post, Ankita Murmu shares her career journey as a Biotechnology graduate, especially the importance of programming in biotechnology and her learning roadmap. Available online: James G., Witten D., Hastie T., Tibshirani R. Tibshirani R. The Lasso Method for Variable Selection in the Cox Model. official website and that any information you provide is encrypted Even though the semantics of these languages is similar, since C influenced C++, C#, Java, Perl and Python directly or indirectly, the philosophy of some of the languages is different and programs should be implemented according to the language paradigm. Bioinformatics, specifically in the context of genomics and molecular pathology, uses computational, mathematical, and statistical tools to collect, organize, and analyze large and complex genetic sequencing data and related biological data. But to achieve such performances generally requires more code because of the reduced standard library. Coding is one of the important skills of the 21st century. Perl and Python allow reading and loading a file in memory in one statement. From the results of the global alignment and NJ programs Python appeared to have better character string manipulation capabilities than Perl. While it is hard to define a learning curve for each language, advantages and disadvantages of each language can be found. Learning R as the first programming language is not as weird as you think. Rawi R., Mall R., Kunji K., Shen C.-H., Kwong P.D., Chuang G.-Y. 2021 Nov 19;2021:4542995. doi: 10.1155/2021/4542995. Both languages use automatic memory management and have large free libraries. Through-out the past years, R was adopted by the bioinformatics community as the number one programming language for the release of new packages, partially because of bioconductor (a collection of mature libraries for next-generation sequencing analysis) and the ggplot2 library for advanced plotting. Life (Basel). In recent years, there has been a huge demand for programming and coding to work with biological datasets. Learning how to code and understand the basics of data science can help you to break into other industries as well. A program using tokenization was written in C as a control to benchmark regular expressions. R is a programming language and software environment designed for statistical computing and graphics. In the NJ program, the performance of C# was similar to C and C++, while Java took significantly more time (Fig (Fig22). Results: Epub 2008 Jan 31. RFPDR: a random forest approach for plant disease resistance protein prediction. The site is secure. What programming languages do bioinformaticians use? - Quora Graphic interfaces are very important in biology, hence it would be interesting to compare the libraries available. Additionally, core biotechnology is a research-oriented career path. Without a subpoena, voluntary compliance on the part of your Internet Service Provider, or additional records from a third party, information stored or retrieved for this purpose alone cannot usually be used to identify you. Comparison of Affymetrix GeneChip expression measures. 4200 Fifth Ave. Stark C., Breitkreutz B.-J., Reguly T., Boucher L., Breitkreutz A., Tyers M. BioGRID: A General Repository for Interaction Datasets.